Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 102106374
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3186644 characters in sequence are not A, C, G, or T
File 121 of 311
Found at i:40334362 original size:14 final size:15
Alignment explanation
Indices: 40334334--40334364 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
40334324 TGAATGATGA
40334334 GTTGATGTCTTGGTT
1 GTTGATGTCTTGGTT
40334349 GTTGATGT-TTGGTT
1 GTTGATGTCTTGGTT
40334363 GT
1 GT
40334365 ATGTATATGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.06, C:0.03, G:0.35, T:0.55
Consensus pattern (15 bp):
GTTGATGTCTTGGTT
Found at i:40337765 original size:36 final size:36
Alignment explanation
Indices: 40337662--40337773 Score: 118
Period size: 36 Copynumber: 3.1 Consensus size: 36
40337652 ACATCAATAT
* *
40337662 TCCAACCAAAACACACCATATGCTCATAAGAGCTAA
1 TCCATCCAAAACACACCAGATGCTCATAAGAGCTAA
* * ** *
40337698 TCCATCTAAAGCACATTAGATGTTCATAAGAGCTAA
1 TCCATCCAAAACACACCAGATGCTCATAAGAGCTAA
** *
40337734 TCCATCCAAAACACACCA-ATGGCTCCGAAGAGCTAG
1 TCCATCCAAAACACACCAGAT-GCTCATAAGAGCTAA
40337770 TCCA
1 TCCA
40337774 ACCGAGACAC
Statistics
Matches: 60, Mismatches: 15, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
35 2 0.03
36 58 0.97
ACGTcount: A:0.39, C:0.29, G:0.12, T:0.20
Consensus pattern (36 bp):
TCCATCCAAAACACACCAGATGCTCATAAGAGCTAA
Found at i:40345901 original size:48 final size:46
Alignment explanation
Indices: 40345781--40345910 Score: 179
Period size: 47 Copynumber: 2.8 Consensus size: 46
40345771 TTCAATCGAT
* *
40345781 AAATACCTATACCATGGCCCGAAGCCAAATCAAGGTAACTTATCCT
1 AAATACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCG
* * *
40345827 AGAGTACCTATACCATGGCCCATAGCCAAATCAAGGTAACTCCTCTCCG
1 A-AATACCTATACCATGGCCCGTAGCCAAATCAAGGTAACT--TATCCG
*
40345876 AAATACCTATACCGTGGCCCGTAGCCAAATCAAGG
1 AAATACCTATACCATGGCCCGTAGCCAAATCAAGG
40345911 CATCACTCAC
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
46 1 0.01
47 36 0.49
48 31 0.42
49 5 0.07
ACGTcount: A:0.34, C:0.30, G:0.16, T:0.20
Consensus pattern (46 bp):
AAATACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTTATCCG
Found at i:40348301 original size:40 final size:40
Alignment explanation
Indices: 40348239--40348454 Score: 323
Period size: 40 Copynumber: 5.4 Consensus size: 40
40348229 AAACCAAGTA
* * *
40348239 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
**
40348278 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
40348318 CCTTCGGGACTTAGCCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
40348358 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40348398 CCTTCGGGACTTAGCCCGGA-ATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
40348438 CCTTCGGGACTTAGCCC
1 CCTTCGGGACTTAGCCC
40348455 CGTTATCATC
Statistics
Matches: 165, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
39 14 0.08
40 151 0.92
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:40361195 original size:33 final size:33
Alignment explanation
Indices: 40361153--40361220 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
40361143 GTGGTGCTTG
40361153 TGAGTAGTTGATTGGTCGTGTTACATGATGACA
1 TGAGTAGTTGATTGGTCGTGTTACATGATGACA
40361186 TGAGTAGTTGATTGGTCGTGTTACATGATGACA
1 TGAGTAGTTGATTGGTCGTGTTACATGATGACA
40361219 TG
1 TG
40361221 TTTACGTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.24, C:0.09, G:0.31, T:0.37
Consensus pattern (33 bp):
TGAGTAGTTGATTGGTCGTGTTACATGATGACA
Found at i:40371332 original size:36 final size:36
Alignment explanation
Indices: 40371285--40371353 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
40371275 ATACACTATT
*
40371285 AGAGTATTTGATGAACTTTCTTACACACCGGTAATC
1 AGAGTATTTGATAAACTTTCTTACACACCGGTAATC
*
40371321 AGAGTATTTGATAAACTTTCTTGCACACCGGTA
1 AGAGTATTTGATAAACTTTCTTACACACCGGTA
40371354 GAGTGTTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (36 bp):
AGAGTATTTGATAAACTTTCTTACACACCGGTAATC
Found at i:40374892 original size:30 final size:30
Alignment explanation
Indices: 40374856--40374914 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
40374846 TCTGAGAGAG
40374856 TAATTCAGATTCTCGAAGATGTGCTTCGTC
1 TAATTCAGATTCTCGAAGATGTGCTTCGTC
40374886 TAATTCAGATTCTCGAAGATGTGCTTCGT
1 TAATTCAGATTCTCGAAGATGTGCTTCGT
40374915 TTTTGTGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (30 bp):
TAATTCAGATTCTCGAAGATGTGCTTCGTC
Found at i:40379334 original size:43 final size:43
Alignment explanation
Indices: 40379235--40379335 Score: 148
Period size: 43 Copynumber: 2.3 Consensus size: 43
40379225 TAGCCTAGCT
* *
40379235 ATGGTCTTACACAAAATCAAATAACGATGCCAATGTTCCAGAC
1 ATGGTCTTACACATAATCAAATAACGATGCCAATGTCCCAGAC
* * * *
40379278 ATGGTTTTACACATAGTCACATAATGATGCCAATGTCCCAGAC
1 ATGGTCTTACACATAATCAAATAACGATGCCAATGTCCCAGAC
40379321 ATGGTCTTACACATA
1 ATGGTCTTACACATA
40379336 TAGACGGGAC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACATAATCAAATAACGATGCCAATGTCCCAGAC
Found at i:40382381 original size:18 final size:20
Alignment explanation
Indices: 40382353--40382389 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
40382343 ATCCCTTTAC
40382353 TTTTAGAAATTTA-TAAAAT
1 TTTTAGAAATTTATTAAAAT
40382372 TTTTAG-AATTTATTAAAA
1 TTTTAGAAATTTATTAAAA
40382390 ATTTATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
TTTTAGAAATTTATTAAAAT
Found at i:40382394 original size:18 final size:19
Alignment explanation
Indices: 40382354--40382394 Score: 50
Period size: 18 Copynumber: 2.2 Consensus size: 19
40382344 TCCCTTTACT
*
40382354 TTTAGAAATTTATAAAATT
1 TTTAGAAATTTATAAAATA
40382373 TTTAG-AATTTATTAAAA-A
1 TTTAGAAATTTA-TAAAATA
40382391 TTTA
1 TTTA
40382395 TTATATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTAGAAATTTATAAAATA
Found at i:40383377 original size:288 final size:288
Alignment explanation
Indices: 40382859--40383434 Score: 1125
Period size: 288 Copynumber: 2.0 Consensus size: 288
40382849 ATATATATAT
40382859 ATAATCAAAATGAACATTTAACGATATAATTTTAATAGAGAGACTATTTTGCTAATTCATCTAAT
1 ATAATCAAAATGAACATTTAACGATATAATTTTAATAGAGAGACTATTTTGCTAATTCATCTAAT
40382924 ATACACAGACTAAATTTTCACATATCTATTTTTCTATATTTTCAGAGAAAGAGAATTAATACATG
66 ATACACAGACTAAATTTTCACATATCTATTTTTCTATATTTTCAGAGAAAGAGAATTAATACATG
40382989 ATAGATTCGATAAATGCAATATGAGATACATTATAGGGACTGATATGGAAAGTTTATCGAAAAAA
131 ATAGATTCGATAAATGCAATATGAGATACATTATAGGGACTGATATGGAAAGTTTATCGAAAAAA
* *
40383054 TATGAACTGTTTTATAATATATAAAAAGCAAAAGAAAATGGGAAGTTCTCAAGTTTTTTTGAATA
196 TATGAACTGTTTTATAATATATAAAAAGAAAAAGAAAATGGGAAGTTCTCAAGTTGTTTTGAATA
40383119 AATGAAAATAAGCCCAATTATTTCAACG
261 AATGAAAATAAGCCCAATTATTTCAACG
40383147 ATAATCAAAATGAACATTTAACGATATAATTTTAATAGAGAGACTATTTTGCTAATTCATCTAAT
1 ATAATCAAAATGAACATTTAACGATATAATTTTAATAGAGAGACTATTTTGCTAATTCATCTAAT
*
40383212 ATACACAGATTAAATTTTCACATATCTATTTTTCTATATTTTCAGAGAAAGAGAATTAATACATG
66 ATACACAGACTAAATTTTCACATATCTATTTTTCTATATTTTCAGAGAAAGAGAATTAATACATG
40383277 ATAGATTCGATAAATGCAATATGAGATACATTATAGGGACTGATATGGAAAGTTTATCGAAAAAA
131 ATAGATTCGATAAATGCAATATGAGATACATTATAGGGACTGATATGGAAAGTTTATCGAAAAAA
40383342 TATGAACTGTTTTATAATATATAAAAAGAAAAAGAAAATGGGAAGTTCTCAAGTTGTTTTGAATA
196 TATGAACTGTTTTATAATATATAAAAAGAAAAAGAAAATGGGAAGTTCTCAAGTTGTTTTGAATA
40383407 AATGAAAATAAGCCCAATTATTTCAACG
261 AATGAAAATAAGCCCAATTATTTCAACG
40383435 GGCTTTAAAT
Statistics
Matches: 285, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
288 285 1.00
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (288 bp):
ATAATCAAAATGAACATTTAACGATATAATTTTAATAGAGAGACTATTTTGCTAATTCATCTAAT
ATACACAGACTAAATTTTCACATATCTATTTTTCTATATTTTCAGAGAAAGAGAATTAATACATG
ATAGATTCGATAAATGCAATATGAGATACATTATAGGGACTGATATGGAAAGTTTATCGAAAAAA
TATGAACTGTTTTATAATATATAAAAAGAAAAAGAAAATGGGAAGTTCTCAAGTTGTTTTGAATA
AATGAAAATAAGCCCAATTATTTCAACG
Found at i:40383810 original size:16 final size:16
Alignment explanation
Indices: 40383789--40383820 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
40383779 CTTTCCATTC
40383789 CCATTTTTGCTTTATA
1 CCATTTTTGCTTTATA
40383805 CCATTTTTGCTTTATA
1 CCATTTTTGCTTTATA
40383821 TCTTATTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.19, G:0.06, T:0.56
Consensus pattern (16 bp):
CCATTTTTGCTTTATA
Found at i:40396160 original size:47 final size:47
Alignment explanation
Indices: 40396082--40396536 Score: 696
Period size: 47 Copynumber: 9.6 Consensus size: 47
40396072 CCCTTCGGGA
* * * * * *
40396082 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40396128 CTCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CT-TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40396176 CTCATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40396223 CTTATCACATAAATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCACAT--ATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40396272 CTTATCACTTATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40396319 CTTATCACATATATACACTTTCACATTCATCACTTCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40396366 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40396415 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40396464 CTTATCACATATATGCACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40396511 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
40396537 CACAATTATC
Statistics
Matches: 379, Mismatches: 24, Indels: 11
0.92 0.06 0.03
Matches are distributed among these distances:
46 2 0.01
47 237 0.63
48 2 0.01
49 138 0.36
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40396279 original size:96 final size:95
Alignment explanation
Indices: 40396082--40396536 Score: 695
Period size: 96 Copynumber: 4.8 Consensus size: 95
40396072 CCCTTCGGGA
* * * * * * *
40396082 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGG-CTCTGTCACAT-ATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT-TATCACATAATATAC
40396145 ACTTTCACATTCATCACATCGGCCATTAGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
*
40396176 CTCATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAAATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT-AATATAC
*
40396241 ACTTTCACATTCATCACATCGGCCATTCGGC
65 ACTTTCACATTCATCACATCGGCCATTAGGC
*
40396272 CTTATCACTTATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAT-ATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAATATACA
*
40396336 CTTTCACATTCATCACTTCGGCCATTAGGC
66 CTTTCACATTCATCACATCGGCCATTAGGC
40396366 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA-ATAT
* *
40396431 ACACTTTCACATTCATCACATTGGCCATTCGGC
63 ACACTTTCACATTCATCACATCGGCCATTAGGC
*
40396464 CTTATCACATATATGCACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATA-ATATAC
40396529 A--TTCACAT
65 ACTTTCACAT
40396537 CACAATTATC
Statistics
Matches: 336, Mismatches: 18, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
94 96 0.29
95 2 0.01
96 196 0.58
98 42 0.12
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (95 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATAATATACA
CTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40396351 original size:143 final size:143
Alignment explanation
Indices: 40396082--40396536 Score: 731
Period size: 143 Copynumber: 3.2 Consensus size: 143
40396072 CCCTTCGGGA
* * * * * *
40396082 CTTATCACAT-T-TATACACTTTCACATCCATCACGTTGGCCACTCGG-CTCTGTCACATATATA
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGCCT-TATCACTTATATA
*
40396144 CACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCAC
65 CACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCAC
40396209 ATCGGCCATTAGGC
130 ATCGGCCATTAGGC
*
40396223 CTTATCACATAAATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACTTATATAC
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACTTATATAC
*
40396288 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACT
66 ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
40396353 TCGGCCATTAGGC
131 TCGGCCATTAGGC
*
40396366 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCAC-T-TATAT
* * *
40396431 ACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATGCACTTTCACATTCATCA
64 ACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCA
40396496 CATCGGCCATTAGGC
129 CATCGGCCATTAGGC
40396511 CTTATCACATATATATACA--TTCACAT
1 CTTATCACATATATATACACTTTCACAT
40396537 CACAATTATC
Statistics
Matches: 294, Mismatches: 15, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
141 10 0.03
143 181 0.62
144 3 0.01
145 100 0.34
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.33
Consensus pattern (143 bp):
CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGCCTTATCACTTATATAC
ACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCCATTAGGC
Found at i:40401799 original size:38 final size:38
Alignment explanation
Indices: 40401743--40401822 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
40401733 GATGTGTATT
* * *
40401743 CGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATC
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
* *
40401781 CGGGATAAATCCTGCAGGCCTAGTGCTGGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
40401819 CGGG
1 CGGG
40401823 CCTTCGAGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
Found at i:40401887 original size:43 final size:43
Alignment explanation
Indices: 40401794--40402011 Score: 307
Period size: 43 Copynumber: 5.1 Consensus size: 43
40401784 GATAAATCCT
* * * *
40401794 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGAG-CTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
40401834 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
40401877 GCAGGCTTAGTGCCGATGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * * *
40401920 GCAGTCTTGGTGCTGGTGATGTGTATTTGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
40401963 GCAGGCTTCGTGTCGGTGATGTGTATTCGGGCCTTCGTTCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
40402006 GCAGGC
1 GCAGGC
40402012 GTAATGCCTG
Statistics
Matches: 159, Mismatches: 16, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
40 15 0.09
41 2 0.01
42 16 0.10
43 126 0.79
ACGTcount: A:0.12, C:0.22, G:0.33, T:0.32
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:40403416 original size:40 final size:40
Alignment explanation
Indices: 40403326--40403502 Score: 207
Period size: 40 Copynumber: 4.5 Consensus size: 40
40403316 ACCCACTTAT
* *** * *
40403326 CTTCGGGATTTAG-CCGGATATAACCACTCGCAC-AAGGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
* * * * * *
40403364 CATCGGGTCTTAGCCCGGATATGGTCACTAGCGCAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
40403404 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
*
40403444 CTTCGGGACTTAGCCCAGA-ATTAGTAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATGC
40403484 CTTCGGGACTTAGCCCGGA
1 CTTCGGGACTTAGCCCGGA
40403503 ATTAATCACT
Statistics
Matches: 118, Mismatches: 18, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
38 10 0.08
39 16 0.14
40 92 0.78
ACGTcount: A:0.25, C:0.28, G:0.24, T:0.23
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGC
Found at i:40403505 original size:40 final size:40
Alignment explanation
Indices: 40403366--40403535 Score: 200
Period size: 40 Copynumber: 4.2 Consensus size: 40
40403356 CACAAGGTCA
* * * *
40403366 TCGGGTCTTAGCCCGGATATGGTCACTAGCGCAAATGCCT
1 TCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCT
*
40403406 TCGGGACTTAGCCCGGATATAGTAACTCGCACAAATGCCT
1 TCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCT
* *
40403446 TCGGGACTTAGCCCAGA-ATTAGTAACTCGCACAAATGCCT
1 TCGGGACTTAGCCCGGATA-TAGTAACTAGCACAAATGCCT
* * * *
40403486 TCGGGACTTAGCCCGGA-ATTAATCACTAGCACCAATGTCT
1 TCGGGACTTAGCCCGGATA-TAGTAACTAGCACAAATGCCT
*
40403526 TTGGGACTTA
1 TCGGGACTTA
40403536 ACCCCGTTAG
Statistics
Matches: 116, Mismatches: 13, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
39 1 0.01
40 115 0.99
ACGTcount: A:0.26, C:0.26, G:0.23, T:0.25
Consensus pattern (40 bp):
TCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCT
Found at i:40405519 original size:38 final size:38
Alignment explanation
Indices: 40405463--40405542 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
40405453 GATGTGTATT
* * *
40405463 CGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATC
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
*
40405501 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
40405539 CGGG
1 CGGG
40405543 CCTTCGTGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
Found at i:40405591 original size:43 final size:43
Alignment explanation
Indices: 40405514--40405745 Score: 353
Period size: 43 Copynumber: 5.4 Consensus size: 43
40405504 GATAAATCCC
* * *
40405514 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
40405555 GCAGGCTTAGTGCCGATGATGTGTATTCGGGGCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
40405598 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
40405641 GCAGGCTTGGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
40405684 GCAGGCTTCA-TACCGGTGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTT-AGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
40405727 GCAGGCGTAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
40405746 AATGATATGT
Statistics
Matches: 175, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
41 14 0.08
42 3 0.02
43 158 0.90
ACGTcount: A:0.13, C:0.23, G:0.34, T:0.29
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:40409605 original size:15 final size:14
Alignment explanation
Indices: 40409570--40409608 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 14
40409560 CCAAACATTC
40409570 AAGAAAAAAAAAGA
1 AAGAAAAAAAAAGA
40409584 AAGAAAAGAAAAAG-
1 AAGAAAA-AAAAAGA
40409598 AAGTAAAAAAA
1 AAG-AAAAAAA
40409609 TTGCAAATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (14 bp):
AAGAAAAAAAAAGA
Found at i:40410252 original size:22 final size:22
Alignment explanation
Indices: 40410220--40410262 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
40410210 GACACGTGAA
40410220 AGATGTCATGGATGCGATCTAC
1 AGATGTCATGGATGCGATCTAC
*
40410242 AGATGTTATGGATGCGATCTA
1 AGATGTCATGGATGCGATCTA
40410263 ACTCCGGAGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.28, C:0.14, G:0.28, T:0.30
Consensus pattern (22 bp):
AGATGTCATGGATGCGATCTAC
Found at i:40416923 original size:48 final size:48
Alignment explanation
Indices: 40416865--40417202 Score: 559
Period size: 48 Copynumber: 7.0 Consensus size: 48
40416855 ATATACACAC
* * *
40416865 ATCTCCTACATATTTCACATTAGCCATTCGGCTTTACCAAATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40416913 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
40416961 ATCTCATATATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
40417009 ATCTCATATATATTTCACATTAGCCATTCGGCTTTACCACATATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* *
40417057 ATCTCATACATATTTCATATTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
*
40417105 ATCTCATACATGTTTCACACTAGCCATTCGGCTTTACCACATATACAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
* * *
40417153 ATCTCATACATATTTCACACTAGCCATTCGGTTTTACCACACATATAT
1 ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
40417201 AT
1 AT
40417203 ATTTATCTTG
Statistics
Matches: 274, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 274 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.36
Consensus pattern (48 bp):
ATCTCATACATATTTCACACTAGCCATTCGGCTTTACCACATATACAT
Found at i:40421439 original size:130 final size:131
Alignment explanation
Indices: 40421290--40421706 Score: 649
Period size: 131 Copynumber: 3.2 Consensus size: 131
40421280 ACTTAAGATG
* * * * *
40421290 TGATCGTAAATCAATGAGCCTTAGTAATATCAGTTGTGATCTTAAATCAACGAGCTGTTTGGAGT
1 TGATTGTAAATCAACGAGCCTTAATAATATTAGTTGTGATCTTAAATCAATGAGCTGTTTGGAGT
*
40421355 AGCGATAGTAAATCAACTAACTTAGAGAAGATTGTTCATGAGAGTAAATCAAAT-AACTTAGGCT
66 AGCGATAGTAAATCAACTAACTTAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCT
40421419 A
131 A
* *
40421420 TGATAGTAAATCAACGAGCCTTAATAATATTAGTTGTGATCTTAAAT-AAGTGAGCTATTTGGAG
1 TGATTGTAAATCAACGAGCCTTAATAATATTAGTTGTGATCTTAAATCAA-TGAGCTGTTTGGAG
* * * *
40421484 TAGCAATAGTAAATCAACTAACTTAGAGAAAATTGTTCATGATAGTAACTCAAATGAACTTAGGT
65 TAGCGATAGTAAATCAACTAACTTAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGC
40421549 TA
130 TA
* *
40421551 TGATTGTAAATCAACGAGCCTTAATAATATTAGTTGTGATCTTAAATCATTGAGATGTTTGGAGT
1 TGATTGTAAATCAACGAGCCTTAATAATATTAGTTGTGATCTTAAATCAATGAGCTGTTTGGAGT
* *
40421616 AGCGATAGTAAATCAACTAACTCAGAAAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCT
66 AGCGATAGTAAATCAACTAACTTAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCT
*
40421681 G
131 A
*
40421682 TGATTGTAAATCACCGAGCCTTAAT
1 TGATTGTAAATCAACGAGCCTTAAT
40421707 TGTAACAACC
Statistics
Matches: 261, Mismatches: 23, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
129 2 0.01
130 106 0.41
131 152 0.58
132 1 0.00
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (131 bp):
TGATTGTAAATCAACGAGCCTTAATAATATTAGTTGTGATCTTAAATCAATGAGCTGTTTGGAGT
AGCGATAGTAAATCAACTAACTTAGAGAAGATTGTTCATGATAGTAAATCAAATGAACTTAGGCT
A
Found at i:40422300 original size:19 final size:19
Alignment explanation
Indices: 40422276--40422318 Score: 86
Period size: 19 Copynumber: 2.3 Consensus size: 19
40422266 GAATATGCCA
40422276 TTGATTATTTTGACTGCTT
1 TTGATTATTTTGACTGCTT
40422295 TTGATTATTTTGACTGCTT
1 TTGATTATTTTGACTGCTT
40422314 TTGAT
1 TTGAT
40422319 GTTAGTAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.16, C:0.09, G:0.16, T:0.58
Consensus pattern (19 bp):
TTGATTATTTTGACTGCTT
Found at i:40424422 original size:54 final size:54
Alignment explanation
Indices: 40424326--40424456 Score: 190
Period size: 54 Copynumber: 2.4 Consensus size: 54
40424316 GATCGTGAGC
* * *
40424326 TACATGGTCACAGTGAGTTACACAGCCTAGCCAAACGGCCATGTAACCTTATTT
1 TACATGGGCACAGTTAGTTACACAGCCTAGCCAAACGACCATGTAACCTTATTT
* * *
40424380 TACATGGGCACAGTTAGTTACACAGCCTGGCCACACGACCATGTGACCTTATTT
1 TACATGGGCACAGTTAGTTACACAGCCTAGCCAAACGACCATGTAACCTTATTT
* *
40424434 TACACGGGCATAGTTAGTTACAC
1 TACATGGGCACAGTTAGTTACAC
40424457 GGTCTGTGTA
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 69 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (54 bp):
TACATGGGCACAGTTAGTTACACAGCCTAGCCAAACGACCATGTAACCTTATTT
Found at i:40427847 original size:43 final size:43
Alignment explanation
Indices: 40427799--40427996 Score: 360
Period size: 43 Copynumber: 4.6 Consensus size: 43
40427789 CCGGTATTAC
40427799 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
40427842 GCCTGCTAGGCACGAAGGCCCGAGTACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
40427885 GCCTGCTAGGCACGAAGGCCTGAATACACATCACCAGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
40427928 GCCTGCTAGGCACGAAGGCCCTAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
40427971 GCCTGCTAGGCACGAAGGCCCGAATA
1 GCCTGCTAGGCACGAAGGCCCGAATA
40427997 TAATACCAGC
Statistics
Matches: 147, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 147 1.00
ACGTcount: A:0.30, C:0.34, G:0.26, T:0.11
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:40428037 original size:38 final size:38
Alignment explanation
Indices: 40427989--40428092 Score: 181
Period size: 38 Copynumber: 2.7 Consensus size: 38
40427979 GGCACGAAGG
* *
40427989 CCCGAATATAATACCAGCACTAGGCCTGCGGGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAT
*
40428027 CCCGGATATAATACCAGCACGAAGCCTGCGGGATTTAT
1 CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAT
40428065 CCCGAATATAATACCAGCACGAAGCCTG
1 CCCGAATATAATACCAGCACGAAGCCTG
40428093 AGGGTCTTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.31, C:0.28, G:0.21, T:0.20
Consensus pattern (38 bp):
CCCGAATATAATACCAGCACGAAGCCTGCGGGATTTAT
Found at i:40430529 original size:25 final size:25
Alignment explanation
Indices: 40430501--40430552 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
40430491 CATTTTCAGA
40430501 AAATTTCACATAGGTCCTATTTCAT
1 AAATTTCACATAGGTCCTATTTCAT
40430526 AAATTTCACATAGGTCCTATTTCAT
1 AAATTTCACATAGGTCCTATTTCAT
40430551 AA
1 AA
40430553 TTTTACTCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (25 bp):
AAATTTCACATAGGTCCTATTTCAT
Found at i:40431559 original size:41 final size:41
Alignment explanation
Indices: 40431479--40431616 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 41
40431469 GAAGATATAA
*
40431479 CAATATCGCACACTTAGTGGCATCACATTAAA-CCAAAGCTATCT
1 CAATATCGCACACTTAGT-GC--CACA-TAAAGCCGAAGCTATCT
* *
40431523 CAGTATCGTACACTTAGTGCCACATAAAGCCGAAGCTAT-T
1 CAATATCGCACACTTAGTGCCACATAAAGCCGAAGCTATCT
* *** *
40431563 CCAAT-TCGCACACTAAGTGCTGTATATAGCCGAAGCTATCT
1 -CAATATCGCACACTTAGTGCCACATAAAGCCGAAGCTATCT
40431604 CGAA-A-CGCACACT
1 C-AATATCGCACACT
40431617 AAGTTCCAAA
Statistics
Matches: 79, Mismatches: 10, Indels: 14
0.77 0.10 0.14
Matches are distributed among these distances:
40 42 0.53
41 19 0.24
43 2 0.03
44 16 0.20
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (41 bp):
CAATATCGCACACTTAGTGCCACATAAAGCCGAAGCTATCT
Found at i:40441019 original size:13 final size:13
Alignment explanation
Indices: 40441001--40441041 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
40440991 TTATATATTC
40441001 AAATTTTACAAAT
1 AAATTTTACAAAT
*
40441014 AAATTTTGA-TAAT
1 AAATTTT-ACAAAT
40441027 AAATTTTACAAAT
1 AAATTTTACAAAT
40441040 AA
1 AA
40441042 TTAATAGTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
12 1 0.04
13 22 0.92
14 1 0.04
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (13 bp):
AAATTTTACAAAT
Found at i:40445031 original size:25 final size:25
Alignment explanation
Indices: 40444997--40445108 Score: 127
Period size: 25 Copynumber: 4.5 Consensus size: 25
40444987 ACCCAAACTT
* *
40444997 GTGAGAGCATACTGATTTACAGCTC
1 GTGAGAGCATACCGATTTATAGCTC
*
40445022 GTGAGAGCATACCGATTTATAGCTT
1 GTGAGAGCATACCGATTTATAGCTC
*
40445047 GTGAGAGCACACCGATTTATAGCTC
1 GTGAGAGCATACCGATTTATAGCTC
** * * *
40445072 AAGTGAGCATATCGATTCATAGCTC
1 GTGAGAGCATACCGATTTATAGCTC
40445097 GT-ATGAGCATAC
1 GTGA-GAGCATAC
40445109 ATATACAGGA
Statistics
Matches: 71, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
25 71 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (25 bp):
GTGAGAGCATACCGATTTATAGCTC
Found at i:40448039 original size:12 final size:12
Alignment explanation
Indices: 40448024--40448077 Score: 65
Period size: 12 Copynumber: 4.4 Consensus size: 12
40448014 TATCAGAACT
*
40448024 AGAATCAAAATG
1 AGAATCAAAATC
40448036 AGAATCAAAATC
1 AGAATCAAAATC
*
40448048 AGAATCAGGTAA-C
1 AGAATCA--AAATC
40448061 AGAATCAAAATC
1 AGAATCAAAATC
40448073 AGAAT
1 AGAAT
40448078 GTGAATGCAA
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 2 0.06
12 24 0.67
13 8 0.22
14 2 0.06
ACGTcount: A:0.56, C:0.13, G:0.15, T:0.17
Consensus pattern (12 bp):
AGAATCAAAATC
Found at i:40448243 original size:27 final size:26
Alignment explanation
Indices: 40448195--40448254 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
40448185 GCGAGGCTGC
*
40448195 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
40448222 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
40448248 AAGATAT
1 CAGATAT
40448255 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:40448611 original size:27 final size:27
Alignment explanation
Indices: 40448581--40449071 Score: 536
Period size: 27 Copynumber: 18.2 Consensus size: 27
40448571 AACACCCTAG
** *
40448581 GGGTAAAATGGTAATTTTATAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
40448608 GGGTAAAAC-GATAATTCTATAAATCGA
1 GGGTAAAACAG-TAATTTTGTAAATCGA
* * *
40448635 GGGTAAAATAGTAATTTTTTAAATTGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
40448662 GGGTAAAACAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* * * *
40448689 CGGTAAAATAGTAATTCTGTCAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
40448716 GGGTAAAAC-GATAATTATGTAAATTGA
1 GGGTAAAACAG-TAATTTTGTAAATCGA
*
40448743 GGGTAAAACAGTAATTTTGTAAATCAA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* **
40448770 GGGTAAAACGGTAATTTTGTAAATTAA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
40448797 AGGTAAAACAGTAATTTTCTAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
*
40448824 GGGTAAAAAAGTAATTTTGTAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* * * *
40448851 GGGTGAAACAGTAATTCTATCAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* * * *
40448878 GGATAAAACGGTAATTCTGTCAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* * *
40448905 GGGTAAAACAATAATTTTATAAATTGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
*
40448932 GGGTAAAACAGTAATTTTATAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* * *
40448959 TGGTAAAACAGTAATTCTATAAATCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* * * *
40448986 GGGTAAAAAAATAATTCTGTAAATCAA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* * * *
40449013 GGGTAAAATAGTAATTCTATAATTCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
* *
40449040 GGGTAAAATAGTAATTTTGTAATTCGA
1 GGGTAAAACAGTAATTTTGTAAATCGA
40449067 GGGTA
1 GGGTA
40449072 CTTTGATAAT
Statistics
Matches: 397, Mismatches: 63, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
26 2 0.01
27 393 0.99
28 2 0.01
ACGTcount: A:0.42, C:0.08, G:0.20, T:0.31
Consensus pattern (27 bp):
GGGTAAAACAGTAATTTTGTAAATCGA
Found at i:40449096 original size:27 final size:26
Alignment explanation
Indices: 40449066--40449194 Score: 107
Period size: 27 Copynumber: 4.8 Consensus size: 26
40449056 TTGTAATTCG
* *
40449066 AGGGTACTTTGATAATTTTACAAGTCA
1 AGGGTA-TTTGGTAATTTTACAAATCA
* * *
40449093 AGGGTATTTCAGTAATTTTGCAAA-CTG
1 AGGGTATTT-GGTAATTTTACAAATC-A
40449120 AGGGTATTTCGGTAATTTTACAAATCA
1 AGGGTATTT-GGTAATTTTACAAATCA
* * * *
40449147 AGGATATTTGGGTAATTTTATAAACCG
1 AGGGTATTT-GGTAATTTTACAAATCA
*
40449174 GGGGTACTTTGGTAATTTTAC
1 AGGGTA-TTTGGTAATTTTAC
40449195 TACTGGGGGT
Statistics
Matches: 82, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
26 4 0.05
27 74 0.90
28 4 0.05
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.38
Consensus pattern (26 bp):
AGGGTATTTGGTAATTTTACAAATCA
Found at i:40449097 original size:54 final size:54
Alignment explanation
Indices: 40449039--40449149 Score: 120
Period size: 54 Copynumber: 2.1 Consensus size: 54
40449029 CTATAATTCG
* * *
40449039 AGGGTAAAAT-AGTAATTTTG-TAATTCGAGGGTACTTT-GATAATTTTACAAGTCA
1 AGGGT-AAATCAGTAATTTTGCAAACT-GAGGGTA-TTTCGATAATTTTACAAATCA
** *
40449093 AGGGTATTTCAGTAATTTTGCAAACTGAGGGTATTTCGGTAATTTTACAAATCA
1 AGGGTAAATCAGTAATTTTGCAAACTGAGGGTATTTCGATAATTTTACAAATCA
40449147 AGG
1 AGG
40449150 ATATTTGGGT
Statistics
Matches: 48, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
53 5 0.10
54 40 0.83
55 3 0.06
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.36
Consensus pattern (54 bp):
AGGGTAAATCAGTAATTTTGCAAACTGAGGGTATTTCGATAATTTTACAAATCA
Found at i:40449155 original size:54 final size:54
Alignment explanation
Indices: 40449064--40449194 Score: 165
Period size: 54 Copynumber: 2.4 Consensus size: 54
40449054 TTTTGTAATT
* * * *
40449064 CGAGGGTACTTTGATAATTTTACAAGTCAAGGGTATTTCAGTAATTTTGCAAAC
1 CGAGGGTACTTTGGTAATTTTACAAATCAAGGATATTTCAGTAATTTTACAAAC
* ** *
40449118 TGAGGGTA-TTTCGGTAATTTTACAAATCAAGGATATTTGGGTAATTTTATAAAC
1 CGAGGGTACTTT-GGTAATTTTACAAATCAAGGATATTTCAGTAATTTTACAAAC
*
40449172 CGGGGGTACTTTGGTAATTTTAC
1 CGAGGGTACTTTGGTAATTTTAC
40449195 TACTGGGGGT
Statistics
Matches: 65, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
53 3 0.05
54 59 0.91
55 3 0.05
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.37
Consensus pattern (54 bp):
CGAGGGTACTTTGGTAATTTTACAAATCAAGGATATTTCAGTAATTTTACAAAC
Found at i:40449214 original size:26 final size:26
Alignment explanation
Indices: 40449065--40449217 Score: 103
Period size: 27 Copynumber: 5.7 Consensus size: 26
40449055 TTTGTAATTC
* *
40449065 GAGGGTACTTT-GATAATTTTACAAGT
1 GAGGGTA-TTTCGGTAATTTTACAACT
* * *
40449091 CAAGGGTATTTCAGTAATTTTGCAAACT
1 -GAGGGTATTTCGGTAATTTTAC-AACT
*
40449119 GAGGGTATTTCGGTAATTTTACAAAT
1 GAGGGTATTTCGGTAATTTTACAACT
* * * * *
40449145 CAAGGATATTTGGGTAATTTTATAAACC
1 -GAGGGTATTTCGGTAATTTTA-CAACT
* *
40449173 GGGGGTACTTT-GGTAATTTTACTACT
1 GAGGGTA-TTTCGGTAATTTTACAACT
* *
40449199 GGGGGTATTTCAGTAATTT
1 GAGGGTATTTCGGTAATTT
40449218 GGTAAACTAA
Statistics
Matches: 98, Mismatches: 22, Indels: 13
0.74 0.17 0.10
Matches are distributed among these distances:
25 3 0.03
26 22 0.22
27 65 0.66
28 8 0.08
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.39
Consensus pattern (26 bp):
GAGGGTATTTCGGTAATTTTACAACT
Found at i:40450798 original size:8 final size:8
Alignment explanation
Indices: 40450785--40450838 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
40450775 GTAGATTGGC
40450785 AAAAGCCG
1 AAAAGCCG
*
40450793 AAAAGCTG
1 AAAAGCCG
**
40450801 AATTGCCG
1 AAAAGCCG
*
40450809 AAAAGTCG
1 AAAAGCCG
40450817 AAAAGCCG
1 AAAAGCCG
40450825 AAATA-CCG
1 AAA-AGCCG
40450833 AAAAGC
1 AAAAGC
40450839 TGAAGAGCTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
7 1 0.03
8 34 0.94
9 1 0.03
ACGTcount: A:0.48, C:0.20, G:0.22, T:0.09
Consensus pattern (8 bp):
AAAAGCCG
Found at i:40450812 original size:24 final size:24
Alignment explanation
Indices: 40450785--40450851 Score: 80
Period size: 24 Copynumber: 2.8 Consensus size: 24
40450775 GTAGATTGGC
* *
40450785 AAAAGCCGAAAAGCTGAATTGCCG
1 AAAAGCCGAAAAGCTGAAATACCG
* *
40450809 AAAAGTCGAAAAGCCGAAATACCG
1 AAAAGCCGAAAAGCTGAAATACCG
* *
40450833 AAAAGCTGAAGAGCTGAAA
1 AAAAGCCGAAAAGCTGAAA
40450852 GTTTGGCTGC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.24, T:0.10
Consensus pattern (24 bp):
AAAAGCCGAAAAGCTGAAATACCG
Found at i:40450824 original size:16 final size:16
Alignment explanation
Indices: 40450785--40450851 Score: 57
Period size: 16 Copynumber: 4.2 Consensus size: 16
40450775 GTAGATTGGC
40450785 AAAAGCCGAAAAGCTG
1 AAAAGCCGAAAAGCTG
**
40450801 AATTGCCGAAAAG-TCG
1 AAAAGCCGAAAAGCT-G
*
40450817 AAAAGCCGAAATA-CCG
1 AAAAGCCGAAA-AGCTG
* *
40450833 AAAAGCTGAAGAGCTG
1 AAAAGCCGAAAAGCTG
40450849 AAA
1 AAA
40450852 GTTTGGCTGC
Statistics
Matches: 39, Mismatches: 8, Indels: 8
0.71 0.15 0.15
Matches are distributed among these distances:
15 2 0.05
16 36 0.92
17 1 0.03
ACGTcount: A:0.48, C:0.18, G:0.24, T:0.10
Consensus pattern (16 bp):
AAAAGCCGAAAAGCTG
Found at i:40451118 original size:29 final size:29
Alignment explanation
Indices: 40451076--40451182 Score: 130
Period size: 29 Copynumber: 3.7 Consensus size: 29
40451066 GAAAGGTGAT
* *
40451076 TTGGGCCTAATGGGTCATATGAATATGAA
1 TTGGGCCTAGTGGGCCATATGAATATGAA
40451105 TTGGGCCTAGTGGGCCATATGAATATGAA
1 TTGGGCCTAGTGGGCCATATGAATATGAA
40451134 TTGGGCCT-GATGGGCCATATG-A-ATGAGA
1 TTGGGCCTAG-TGGGCCATATGAATATGA-A
* * *
40451162 TTGGGCCAAATAGGCCATATG
1 TTGGGCCTAGTGGGCCATATG
40451183 CATGTATATA
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
27 4 0.06
28 20 0.29
29 46 0.66
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.27
Consensus pattern (29 bp):
TTGGGCCTAGTGGGCCATATGAATATGAA
Found at i:40455995 original size:24 final size:24
Alignment explanation
Indices: 40455966--40456059 Score: 134
Period size: 24 Copynumber: 3.9 Consensus size: 24
40455956 TATTGACATT
*
40455966 CAAATCCGCACATATAGTGCCATA
1 CAAATCCGCACACATAGTGCCATA
* *
40455990 CAAATCCACACACATAGTGCCGTA
1 CAAATCCGCACACATAGTGCCATA
* *
40456014 CAAATTCGCACACATAGTGCCATT
1 CAAATCCGCACACATAGTGCCATA
*
40456038 CAAATTCGCACACATAGTGCCA
1 CAAATCCGCACACATAGTGCCA
40456060 AAATCATTTC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.36, C:0.31, G:0.13, T:0.20
Consensus pattern (24 bp):
CAAATCCGCACACATAGTGCCATA
Found at i:40456005 original size:48 final size:48
Alignment explanation
Indices: 40455923--40456056 Score: 133
Period size: 48 Copynumber: 2.8 Consensus size: 48
40455913 CCATGTTTAC
* * ** * * * *
40455923 CCGCACACATAGTGACTTAGTAATTCACATACATATTGACATTCAAAT
1 CCGCACACATAGTGCCATACAAATCCACACACATAGTGACATACAAAT
* * *
40455971 CCGCACATATAGTGCCATACAAATCCACACACATAGTGCCGTACAAAT
1 CCGCACACATAGTGCCATACAAATCCACACACATAGTGACATACAAAT
* * * *
40456019 TCGCACACATAGTGCCATTCAAATTCGCACACATAGTG
1 CCGCACACATAGTGCCATACAAATCCACACACATAGTG
40456057 CCAAAATCAT
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 70 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.24
Consensus pattern (48 bp):
CCGCACACATAGTGCCATACAAATCCACACACATAGTGACATACAAAT
Found at i:40456029 original size:72 final size:72
Alignment explanation
Indices: 40455926--40456059 Score: 178
Period size: 72 Copynumber: 1.9 Consensus size: 72
40455916 TGTTTACCCG
* ** * * *
40455926 CACACATAGTGACTTAGTAATTCACATACATATTGACATTCAAATCCGCACATATAGTGCCATAC
1 CACACATAGTGACGTACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCATAC
40455991 AAATCCA
66 AAATCCA
* * * *
40455998 CACACATAGTGCCGTACAAATTCGCACACATAGTGCCATTCAAATTCGCACACATAGTGCCA
1 CACACATAGTGACGTACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCA
40456060 AAATCATTTC
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
72 52 1.00
ACGTcount: A:0.37, C:0.28, G:0.12, T:0.24
Consensus pattern (72 bp):
CACACATAGTGACGTACAAATTCACACACATAGTGACATTCAAATCCGCACACATAGTGCCATAC
AAATCCA
Found at i:40457330 original size:15 final size:14
Alignment explanation
Indices: 40457304--40457339 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
40457294 CCTTTTATTC
*
40457304 TTTTATTCATTCAT
1 TTTTATTAATTCAT
40457318 TTCTTATTAATTCAT
1 TT-TTATTAATTCAT
40457333 TTTTATT
1 TTTTATT
40457340 TGGATTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.22, C:0.11, G:0.00, T:0.67
Consensus pattern (14 bp):
TTTTATTAATTCAT
Found at i:40458800 original size:29 final size:29
Alignment explanation
Indices: 40458767--40458873 Score: 139
Period size: 29 Copynumber: 3.7 Consensus size: 29
40458757 TAAAGGTGTT
*
40458767 TTGGGCCTAATGGGTCATATGAATATGAA
1 TTGGGCCTAATGGGCCATATGAATATGAA
*
40458796 TTGGGCCTAATGGGCCATATGAATGTGAA
1 TTGGGCCTAATGGGCCATATGAATATGAA
* *
40458825 TTGGGCCTGATGGGCTATATG-A-ATGAGA
1 TTGGGCCTAATGGGCCATATGAATATGA-A
40458853 TTGGGCC-AAGTGGGCCATATG
1 TTGGGCCTAA-TGGGCCATATG
40458874 CATGTATGTA
Statistics
Matches: 69, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
27 4 0.06
28 19 0.28
29 46 0.67
ACGTcount: A:0.26, C:0.13, G:0.33, T:0.28
Consensus pattern (29 bp):
TTGGGCCTAATGGGCCATATGAATATGAA
Found at i:40459177 original size:27 final size:26
Alignment explanation
Indices: 40459130--40459184 Score: 65
Period size: 27 Copynumber: 2.1 Consensus size: 26
40459120 GAAACCATAT
* ** *
40459130 TAAGGGGAAAATTACTGAAATGCCCC
1 TAAGGGGAAAATGACCAAAATACCCC
40459156 TAAGGGCGAAAATGACCAAAATACCCC
1 TAAGGG-GAAAATGACCAAAATACCCC
40459183 TA
1 TA
40459185 GGTGTTGAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
26 6 0.25
27 18 0.75
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (26 bp):
TAAGGGGAAAATGACCAAAATACCCC
Found at i:40465367 original size:25 final size:25
Alignment explanation
Indices: 40465322--40465410 Score: 103
Period size: 25 Copynumber: 3.6 Consensus size: 25
40465312 TGACCCACAA
* *
40465322 CTCGTAAGAGCATACCAATTTATAG
1 CTCGTGAGAGCATACCAATTTACAG
*
40465347 CTTGTGAGAGCATA-CAGATTTACAG
1 CTCGTGAGAGCATACCA-ATTTACAG
40465372 CTCGTGAGAGC-T-CCAATTTACAG
1 CTCGTGAGAGCATACCAATTTACAG
* *
40465395 CTCGAGTGAGCATACC
1 CTCGTGAGAGCATACC
40465411 GATTCACATC
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
23 17 0.31
24 6 0.11
25 31 0.57
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.26
Consensus pattern (25 bp):
CTCGTGAGAGCATACCAATTTACAG
Found at i:40474379 original size:40 final size:39
Alignment explanation
Indices: 40474302--40474387 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 39
40474292 TAACAACTTA
**
40474302 TCGGCTAAAATGACACTTAGTGTGCGGTTCGAAATAGCT
1 TCGGCTAAAATGACACTTAGTGTGCAATTCGAAATAGCT
* * * * *
40474341 TTGGCTAAAAGTGGCACTTGGTGTGCAATTTGAGATAGCT
1 TCGGCTAAAA-TGACACTTAGTGTGCAATTCGAAATAGCT
40474381 TCGGCTA
1 TCGGCTA
40474388 TATTTATATA
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
39 9 0.24
40 29 0.76
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (39 bp):
TCGGCTAAAATGACACTTAGTGTGCAATTCGAAATAGCT
Found at i:40477299 original size:50 final size:50
Alignment explanation
Indices: 40477193--40477366 Score: 180
Period size: 50 Copynumber: 3.6 Consensus size: 50
40477183 CATGTGAGCT
* * * * *
40477193 AGTGTAAGACCATGTCTAGGACATGGCATTGG-CTTGAT---A-TGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAGAAGAGAGTC
* ** *
40477238 AGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-GGATAGGGGAGAGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGATAGAAGAGAGTC
* *
40477288 AGTGTAAGACCATGTCTGGGATATGGCATCGGCCTCGATATAAGAGAGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAGAAGAGAGTC
* *
40477338 AGTGTAAGACTATGTTTGGGACATGGCAT
1 AGTGTAAGACCATGTCTGGGACATGGCAT
40477367 TGACTGGATA
Statistics
Matches: 106, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
45 30 0.28
46 3 0.03
47 1 0.01
49 1 0.01
50 71 0.67
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.26
Consensus pattern (50 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAGAAGAGAGTC
Found at i:40486854 original size:48 final size:48
Alignment explanation
Indices: 40486783--40486910 Score: 195
Period size: 48 Copynumber: 2.7 Consensus size: 48
40486773 TGATATGTGT
*
40486783 GCTAGTGTAAGACCATGTGTGGGACATGGCATCAGCCAC-ATTATGAGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACTA-TATGAGA
** *
40486831 GCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCTTCTATATGTGA
1 GCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACTATATGAGA
*
40486879 GCCAGTGTAAGACCATGTCTGGGACATGGCAT
1 GCTAGTGTAAGACCATGTCTGGGACATGGCAT
40486911 TAGCAGTTTA
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
48 73 0.99
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.25
Consensus pattern (48 bp):
GCTAGTGTAAGACCATGTCTGGGACATGGCATCAGCCACTATATGAGA
Found at i:40488557 original size:24 final size:24
Alignment explanation
Indices: 40488525--40488595 Score: 115
Period size: 24 Copynumber: 3.0 Consensus size: 24
40488515 CTGTCAGGAG
40488525 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
40488549 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
* **
40488573 AGTATTTAGGAGCAGATAAGGGA
1 AGGATTTAGGAGTTGATAAGGGA
40488596 GGAAATCTAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 44 1.00
ACGTcount: A:0.35, C:0.01, G:0.37, T:0.27
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:40490052 original size:27 final size:26
Alignment explanation
Indices: 40490012--40490116 Score: 120
Period size: 27 Copynumber: 3.9 Consensus size: 26
40490002 AGAAAGCGTC
*
40490012 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGAT
*
40490039 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGAT
*
40490066 CTGGTGGTTCTGCCACGATTATCTGTAT
1 CTGGTGGCTCTGCCAC-ATTATCTG-AT
* **
40490094 CTGGTGACTCTATCACATTATCT
1 CTGGTGGCTCTGCCACATTATCT
40490117 TTTCTAGCAG
Statistics
Matches: 67, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.03
27 50 0.75
28 15 0.22
ACGTcount: A:0.18, C:0.24, G:0.21, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGAT
Found at i:40490116 original size:54 final size:54
Alignment explanation
Indices: 40490012--40490121 Score: 141
Period size: 54 Copynumber: 2.0 Consensus size: 54
40490002 AGAAAGCGTC
* *
40490012 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTACCACATATATCTGTT
* * * * *
40490066 CTGGTGGTTCTGCCACGATTATCTGTATCTGGTGACTCTATCACAT-TATCTTTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTACCACATATATCTGTT
40490120 CT
1 CT
40490122 AGCAGCCATG
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
54 31 0.65
55 17 0.35
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTACCACATATATCTGTT
Found at i:40497753 original size:30 final size:30
Alignment explanation
Indices: 40497719--40497815 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
40497709 TAAACTAAAA
40497719 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
40497749 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
40497779 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
40497809 TGAGCTA
1 TGAGCTA
40497816 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:40502471 original size:30 final size:30
Alignment explanation
Indices: 40502437--40502533 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
40502427 TAAACTAAAA
40502437 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
* * * * * *
40502467 TGAGCTGAGGC-TAAACTCCTAAGCTGAAGT
1 TGAGCT-AAGCTTTAGCTCGTGAGCTAAAGT
* *
40502497 TGAGCTAAGGTTTAGCTCGTGAGTTGAAAG-
1 TGAGCTAAGCTTTAGCTCGTGAGCT-AAAGT
40502527 TGAGCTA
1 TGAGCTA
40502534 GGAGTGAGCT
Statistics
Matches: 50, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
29 2 0.04
30 42 0.84
31 6 0.12
ACGTcount: A:0.28, C:0.15, G:0.29, T:0.28
Consensus pattern (30 bp):
TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
Found at i:40502883 original size:24 final size:24
Alignment explanation
Indices: 40502813--40502871 Score: 118
Period size: 24 Copynumber: 2.5 Consensus size: 24
40502803 CTGTCAAGAG
40502813 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
40502837 AGGATTTAGGAGTTGATAAGGGAT
1 AGGATTTAGGAGTTGATAAGGGAT
40502861 AGGATTTAGGA
1 AGGATTTAGGA
40502872 ACAGATAAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.37, T:0.29
Consensus pattern (24 bp):
AGGATTTAGGAGTTGATAAGGGAT
Found at i:40504341 original size:27 final size:26
Alignment explanation
Indices: 40504301--40504412 Score: 125
Period size: 27 Copynumber: 4.2 Consensus size: 26
40504291 AGGAAGCGTC
40504301 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTATGCCAC-ATTATCTGAT
* *
40504328 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAT-TATCTGAT
*
40504355 CTGGTGGTTATGCCACGATTATCTGTAT
1 CTGGTGGCTATGCCAC-ATTATCTG-AT
* * * *
40504383 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACATTATCTGAT
40504409 CTGG
1 CTGG
40504413 CAGCCATGCT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
26 7 0.10
27 50 0.69
28 15 0.21
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (26 bp):
CTGGTGGCTATGCCACATTATCTGAT
Found at i:40504405 original size:54 final size:54
Alignment explanation
Indices: 40504301--40504412 Score: 172
Period size: 54 Copynumber: 2.1 Consensus size: 54
40504291 AGGAAGCGTC
*
40504301 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
* * *
40504355 CTGGTGGTTATGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTT
1 CTGGTGGCTATGCCACAATTATCTG-ATCTGGTGACTCTGCCACATATATCTGTT
40504409 CTGG
1 CTGG
40504413 CAGCCATGCT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
54 35 0.66
55 18 0.34
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.38
Consensus pattern (54 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATATATCTGTT
Found at i:40504434 original size:54 final size:55
Alignment explanation
Indices: 40504310--40504434 Score: 130
Period size: 54 Copynumber: 2.3 Consensus size: 55
40504300 CCTGGTGGCT
* * * ** **
40504310 ATGCCACAATTATCTG-ATCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGTT
1 ATGCCACGATAATCTGTATCTGGTGACTCTGCCACATATATCTGTTCTGGCAGCC
* *
40504364 ATGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCTGTTCTGGCAGCC
1 ATGCCACGATAATCTGTATCTGGTGACTCTGCCACATATATCTGTTCTGGCAGCC
*
40504418 ATGCTAC-ATAATTCTGT
1 ATGCCACGATAA-TCTGT
40504435 GGCGTGTAGC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
53 3 0.05
54 39 0.65
55 18 0.30
ACGTcount: A:0.20, C:0.23, G:0.20, T:0.37
Consensus pattern (55 bp):
ATGCCACGATAATCTGTATCTGGTGACTCTGCCACATATATCTGTTCTGGCAGCC
Found at i:40507635 original size:119 final size:120
Alignment explanation
Indices: 40507453--40507668 Score: 278
Period size: 119 Copynumber: 1.8 Consensus size: 120
40507443 TCCTCGTTCA
** *
40507453 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
* *
40507518 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACC
* * **
40507573 AATGCCTTCGGG-CTTAGCCCGAA-ATTAGTATCTCGCACAAATACCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGAATA-TAGTAACTCGCACAAATACCTTCGGGA-CTTAACCCGG
* *
40507635 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTA
40507669 GCCCGGACAT
Statistics
Matches: 82, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
118 4 0.05
119 58 0.71
120 20 0.24
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGAATATAGTAACTCGCACAAATACCTTCGGGACTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACC
Found at i:40507659 original size:79 final size:79
Alignment explanation
Indices: 40507451--40507673 Score: 225
Period size: 79 Copynumber: 2.8 Consensus size: 79
40507441 GCTCCTCGTT
* * * * * * * *
40507451 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGG
1 CAAATACCTTCGGGACTTAACCCAGATATAGTAACTAGCACAAA-GCCTTCGGGACTTAGCCCGA
*
40507516 ATTTAGTAACTCGCA
65 AATTAGTAACTCGCA
* * * *
40507531 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGA
1 CAAATACCTTCGGGACTTAACCCAGATATAGTAACTAGCA-CAAAGCCTTCGGGACTTAGCCCGA
*
40507595 AATTAGTATCTCGCA
65 AATTAGTAACTCGCA
** * * *
40507610 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATACCTTCGGGA-CTTAACCCAGATATAGTAAC-TAGCACAAAGCCTTCGGGACTTAGCCCG
40507674 GACATCATTC
Statistics
Matches: 120, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
78 3 0.03
79 57 0.47
80 57 0.47
81 3 0.03
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATACCTTCGGGACTTAACCCAGATATAGTAACTAGCACAAAGCCTTCGGGACTTAGCCCGAA
ATTAGTAACTCGCA
Found at i:40507675 original size:40 final size:40
Alignment explanation
Indices: 40507451--40507675 Score: 260
Period size: 40 Copynumber: 5.7 Consensus size: 40
40507441 GCTCCTCGTT
* *
40507451 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
40507491 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
40507531 CAAATGCCTTCGGGACTTAACCCAGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* * *
40507571 CCAATGCCTTCGGG-CTTAGCCC-GAAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * * *
40507610 CAAATACCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
40507651 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
40507676 CATCATTCAA
Statistics
Matches: 159, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
38 4 0.03
39 27 0.17
40 114 0.72
41 14 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:40510436 original size:26 final size:26
Alignment explanation
Indices: 40510401--40510451 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
40510391 ATGTGAAAAG
*
40510401 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
40510427 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
40510452 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:40510539 original size:26 final size:26
Alignment explanation
Indices: 40510504--40510554 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
40510494 AATGTGAAAG
*
40510504 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
40510530 GGGGTTGCTAAGTGCTGATTCCCCG
1 GGGGTTGCTAAGTGCTGATTCCCCG
40510555 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.12, C:0.24, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:40510555 original size:103 final size:103
Alignment explanation
Indices: 40510322--40510688 Score: 623
Period size: 103 Copynumber: 3.6 Consensus size: 103
40510312 TTGTATATAA
** *
40510322 AGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
40510386 TTGAAATGTGAAAAGGGGGTTGCTATGTGCTGATTCCCCG
65 TTGAAATGTG-AAAGGGGGTTGCTATGTGCTGATTCCCCG
*
40510426 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
40510491 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
*
40510529 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
40510594 TGAAA--TGAAAGGGGGTTGCTATGTGCTGATTCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
** *
40510630 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGCGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
40510689 ATAACGGTTA
Statistics
Matches: 254, Mismatches: 8, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
101 86 0.34
103 99 0.39
104 68 0.27
105 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (103 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCG
Found at i:40510640 original size:26 final size:26
Alignment explanation
Indices: 40510605--40510656 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
40510595 GAAATGAAAG
*
40510605 GGGGTTGCTATGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
40510631 GGGGTTGCTAAGTGCTGATTCCCCGA
1 GGGGTTGCTAAGTGCTGATTCCCCGA
40510657 TTCAGCGGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.13, C:0.23, G:0.35, T:0.29
Consensus pattern (26 bp):
GGGGTTGCTAAGTGCTGATTCCCCGA
Found at i:40518888 original size:46 final size:46
Alignment explanation
Indices: 40518836--40518964 Score: 199
Period size: 46 Copynumber: 2.8 Consensus size: 46
40518826 ATGTAACCCG
* * *
40518836 CCATAAGCGAACTCGGACTCAACTCAA-GAGCTCGG-CGTTCGGCATT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTC-GCA-T
40518882 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
40518928 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
40518965 TGCTCAACTC
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
46 64 0.82
47 10 0.13
48 4 0.05
ACGTcount: A:0.29, C:0.29, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:40523154 original size:12 final size:12
Alignment explanation
Indices: 40523137--40523162 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40523127 CCGGCACTGA
40523137 TTCAACTTTCTT
1 TTCAACTTTCTT
40523149 TTCAACTTTCTT
1 TTCAACTTTCTT
40523161 TT
1 TT
40523163 GTATTAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.15, C:0.23, G:0.00, T:0.62
Consensus pattern (12 bp):
TTCAACTTTCTT
Found at i:40530685 original size:46 final size:46
Alignment explanation
Indices: 40530635--40530807 Score: 173
Period size: 46 Copynumber: 3.8 Consensus size: 46
40530625 TGGTTGAGCA
40530635 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
40530681 TCCGAACTCGTTGAGTTGAGTCCGAGTT--C--GTGGATG-TAATAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAT--G
* *
40530724 CATCCGAACT--TTGTGGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTG-AGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
40530771 -CCAGAGCTCATTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40530808 CGGGTTACAT
Statistics
Matches: 105, Mismatches: 9, Indels: 26
0.75 0.06 0.19
Matches are distributed among these distances:
41 3 0.03
42 6 0.06
43 4 0.04
44 17 0.16
45 12 0.11
46 51 0.49
47 4 0.04
48 6 0.06
49 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:40530785 original size:90 final size:90
Alignment explanation
Indices: 40530632--40530800 Score: 261
Period size: 90 Copynumber: 1.9 Consensus size: 90
40530622 GGATGGTTGA
* *
40530632 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTC-TTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAGT
40530697 TGAGTCCGAGTTCGTGGATGTAATAG
65 TGAGTCCGAGTTCGTGGATGTAATAG
* *
40530723 GCATCCGAACT-TTGTGGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCAGAGCTCATTGAG
1 GCATCCGAACTCTTG-AGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCATTGAG
40530786 TTGAGTCCGAGTTCG
64 TTGAGTCCGAGTTCG
40530801 CTTATGGCGG
Statistics
Matches: 72, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
89 5 0.07
90 56 0.78
91 11 0.15
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (90 bp):
GCATCCGAACTCTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCATTGAGTT
GAGTCCGAGTTCGTGGATGTAATAG
Found at i:40533402 original size:16 final size:17
Alignment explanation
Indices: 40533371--40533403 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40533361 TAACATCATA
*
40533371 AATTTCTTTACTTCTTC
1 AATTTCTATACTTCTTC
40533388 AATTTCTAT-CTTCTTC
1 AATTTCTATACTTCTTC
40533404 TTTATTCCCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (17 bp):
AATTTCTATACTTCTTC
Found at i:40533675 original size:46 final size:44
Alignment explanation
Indices: 40533571--40533678 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
40533561 TGTCTTTGAC
** * * *
40533571 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
40533615 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
40533661 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
40533679 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:40535692 original size:21 final size:21
Alignment explanation
Indices: 40535667--40535710 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
40535657 TTGTAAAGTT
40535667 TAGTCACATTTTGTATCGAGG
1 TAGTCACATTTTGTATCGAGG
40535688 TAGTCACATTTTGTATCGAGG
1 TAGTCACATTTTGTATCGAGG
40535709 TA
1 TA
40535711 AGTTTACAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (21 bp):
TAGTCACATTTTGTATCGAGG
Found at i:40536011 original size:48 final size:48
Alignment explanation
Indices: 40535908--40536019 Score: 129
Period size: 48 Copynumber: 2.3 Consensus size: 48
40535898 GACAGAAATG
*
40535908 AGTCATGTAAGTCCATATCAGATATATATGGCTTTGGAGAACAGGATG
1 AGTCATGTAAGTCCATATCAGATATATATGGCTTTGGAGAACAGGATA
* * * * *
40535956 AGCCATGTAAGCCCATATTATATATATATGG-TATTGG-GAGCAGGAATA
1 AGTCATGTAAGTCCATATCAGATATATATGGCT-TTGGAGAACAGG-ATA
*
40536004 ATTCATGTAAGTCCAT
1 AGTCATGTAAGTCCAT
40536020 GTCGAAGACA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
47 7 0.13
48 46 0.87
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.30
Consensus pattern (48 bp):
AGTCATGTAAGTCCATATCAGATATATATGGCTTTGGAGAACAGGATA
Found at i:40543217 original size:104 final size:104
Alignment explanation
Indices: 40543038--40543402 Score: 609
Period size: 104 Copynumber: 3.6 Consensus size: 104
40543028 TTGTATATAA
** *
40543038 AGGGGTTGCTGTGTGCTGATTCCCCGATTCA-TGGTGGTGCTATGTGCG-TGATCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGAT-ATCCACCATATCT
40543101 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
40543141 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
40543206 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
40543245 AGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATAT---CCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
40543307 TGAAA--TGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* *
40543344 AGGGGTTGCTAAGTGCTGATTCCCCGATTCAGTGGTGGTGCTAAGTGCGAGATCCACCA
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCA
40543403 ATAACGGTAA
Statistics
Matches: 250, Mismatches: 7, Indels: 11
0.93 0.03 0.04
Matches are distributed among these distances:
99 82 0.33
101 14 0.06
102 3 0.01
103 28 0.11
104 122 0.49
105 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.31, T:0.30
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCATATCTT
TGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:40547682 original size:48 final size:48
Alignment explanation
Indices: 40547568--40548073 Score: 618
Period size: 48 Copynumber: 10.6 Consensus size: 48
40547558 AGGTCCCGTA
* * *
40547568 TAAGACCATGTCTGGGACATGGCATCGGCATCGATATGAGA-CCCGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGAGCCAGTG
* * *
40547615 TAAGAACATGTCTAGGACATGGCATCGACATTGATATGTGAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGAGCCAGTG
* * * *** *
40547663 TAAGACCATGTCTGAGACATAGCATTGTTGTTGATATGTGAGCCAATG
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGAGCCAGTG
* * *
40547711 TAATACCATGTCTGGGACATGGCATCGGCGTGGATATGTGAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGAGCCAGTG
** *
40547759 TAAGACCATGTCTGGGACATGGCATCGGTGTTGATATGTGAGCCACTG
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGAGCCAGTG
* * * *
40547807 TAAGACCATGCCTAGGACATGGCATCGGCATTAATATTTGAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGAGCCAGTG
* * ** *
40547855 TAAGACCATGTCTGGGATATGGCATCAGTGTGGATATGTGAGCCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGAGCCAGTG
* ** *
40547903 TAAGACCATGTCTGGGACATGGCATCAGTGTTGATATGTGAACCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGAGCCAGTG
* * *
40547951 TAAGACCATGTTTGGGACATGGCATCGGTATTGATATGTGAACCAGTG
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGAGCCAGTG
* * * * * * * *
40547999 TAAGACGATGTTTGGGACATGGCATCGGTACTAATATGTGTGCTAATG
1 TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGAGCCAGTG
40548047 TAAGACCATGTCTGGGACATGGCATCG
1 TAAGACCATGTCTGGGACATGGCATCG
40548074 ACACTGACAT
Statistics
Matches: 400, Mismatches: 58, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
47 36 0.09
48 364 0.91
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (48 bp):
TAAGACCATGTCTGGGACATGGCATCGGCATTGATATGTGAGCCAGTG
Found at i:40553916 original size:17 final size:17
Alignment explanation
Indices: 40553894--40553938 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
40553884 AATAGCGTGG
40553894 TGTTTTGAAAACATTTA
1 TGTTTTGAAAACATTTA
40553911 TGTTTTGAAAACATTTA
1 TGTTTTGAAAACATTTA
*
40553928 TCTTTTGAAAA
1 TGTTTTGAAAA
40553939 TTCGTGTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (17 bp):
TGTTTTGAAAACATTTA
Found at i:40558351 original size:44 final size:44
Alignment explanation
Indices: 40558301--40558479 Score: 168
Period size: 43 Copynumber: 4.0 Consensus size: 44
40558291 TATATTGTAG
40558301 ATTGGCACTAAGTGTGTGAGACTGAGATAGCTTCAGCTAAATAT
1 ATTGGCACTAAGTGTGTGAGACTGAGATAGCTTCAGCTAAATAT
* *
40558345 ATTGGCACTAAGTGTGTGAGAC-AAGATAGCTTCGGCTAAATACT
1 ATTGGCACTAAGTGTGTGAGACTGAGATAGCTTCAGCTAAATA-T
* * * * * *
40558389 -TTGGCACTAAGTATGCGAGA-TCAAATAACTTCGGCTGTATACATAT
1 ATTGGCACTAAGTGTGTGAGACTGAGATAGCTTCAGC--TA-A-ATAT
* * * *
40558435 ATTGGCACTTAGTGTGTGTA-ATTGAGATAGCTCCAGCTATATAT
1 ATTGGCACTAAGTGTGTG-AGACTGAGATAGCTTCAGCTAAATAT
40558479 A
1 A
40558480 CATATTAGAT
Statistics
Matches: 110, Mismatches: 16, Indels: 18
0.76 0.11 0.12
Matches are distributed among these distances:
43 47 0.43
44 28 0.25
45 2 0.02
46 4 0.04
47 18 0.16
48 11 0.10
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Consensus pattern (44 bp):
ATTGGCACTAAGTGTGTGAGACTGAGATAGCTTCAGCTAAATAT
Found at i:40558386 original size:43 final size:43
Alignment explanation
Indices: 40558301--40558452 Score: 173
Period size: 43 Copynumber: 3.4 Consensus size: 43
40558291 TATATTGTAG
* *
40558301 ATTGGCACTAAGTGTGTGAGACTGAGATAGCTTCAGCTAAATAT
1 ATTGGCACTAAGTGTGTGAGAC-AAGATAGCTTCGGCTAAATAT
40558345 ATTGGCACTAAGTGTGTGAGACAAGATAGCTTCGGCTAAATACT
1 ATTGGCACTAAGTGTGTGAGACAAGATAGCTTCGGCTAAATA-T
* * *
40558389 -TTGGCACTAAGTATGCGAGATCAA-ATAACTTCGGCTGTATACATAT
1 ATTGGCACTAAGTGTGTGAGA-CAAGATAGCTTCGGC--TA-A-ATAT
*
40558435 ATTGGCACTTAGTGTGTG
1 ATTGGCACTAAGTGTGTG
40558453 TAATTGAGAT
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
43 46 0.49
44 26 0.28
45 2 0.02
46 2 0.02
47 17 0.18
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (43 bp):
ATTGGCACTAAGTGTGTGAGACAAGATAGCTTCGGCTAAATAT
Found at i:40559735 original size:17 final size:16
Alignment explanation
Indices: 40559702--40559736 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
40559692 ATGAAAGCTA
*
40559702 TTTCAATTGTTGAAGT
1 TTTCAATTGTCGAAGT
40559718 TTTCAATTGTGCGAAGT
1 TTTCAATTGT-CGAAGT
40559735 TT
1 TT
40559737 GATTTGGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.49
Consensus pattern (16 bp):
TTTCAATTGTCGAAGT
Found at i:40560622 original size:43 final size:43
Alignment explanation
Indices: 40560534--40560668 Score: 180
Period size: 43 Copynumber: 3.1 Consensus size: 43
40560524 ATATATATTG
* * *
40560534 TACATTGGCACTAAGTGTGCGAGACTGAGATAGCTCCGGCTAAA
1 TACATTGGCACTAAGTGTGCGAGAC-CAGATAGCTTCAGCTAAA
*
40560578 TATATTGGCACTAAGTGTGCGAGACCAGATAGCTTCAGCTAAA
1 TACATTGGCACTAAGTGTGCGAGACCAGATAGCTTCAGCTAAA
* * * * *
40560621 TACATTGGCACTAAGTGTGCGAAATCAGATAACTTTAGCTATA
1 TACATTGGCACTAAGTGTGCGAGACCAGATAGCTTCAGCTAAA
40560664 TACAT
1 TACAT
40560669 ATATTGGAAC
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
43 57 0.70
44 24 0.30
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.27
Consensus pattern (43 bp):
TACATTGGCACTAAGTGTGCGAGACCAGATAGCTTCAGCTAAA
Found at i:40562692 original size:48 final size:47
Alignment explanation
Indices: 40562553--40562718 Score: 172
Period size: 48 Copynumber: 3.5 Consensus size: 47
40562543 GGGTGTTACA
* * *
40562553 ATGTCTAGGACATGGCATCGGCCAC-ATTATGAGAGCCAGTGTAAGAGC
1 ATGTCTAGGACATGGCATCGGCCTCGA-CATG-GAGCCAGTGTAAGAAC
* * ** * * *
40562601 ATGTCTGGGACATGGCATTGGTATTGAGACTGGAGCTAGTGTAAGAAC
1 ATGTCTAGGACATGGCATCGGCCTCGACA-TGGAGCCAGTGTAAGAAC
* * *
40562649 ATGTCTAGGACATGGCATCAGCCTCGACATGTGAGCCAATGTAAGACC
1 ATGTCTAGGACATGGCATCGGCCTCGACATG-GAGCCAGTGTAAGAAC
40562697 ATGTCTAGGACATGGCATCGGC
1 ATGTCTAGGACATGGCATCGGC
40562719 AATTTACCCT
Statistics
Matches: 95, Mismatches: 20, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
47 2 0.02
48 90 0.95
49 3 0.03
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.23
Consensus pattern (47 bp):
ATGTCTAGGACATGGCATCGGCCTCGACATGGAGCCAGTGTAAGAAC
Found at i:40565988 original size:33 final size:33
Alignment explanation
Indices: 40565946--40566011 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
40565936 TCTATTCTAA
40565946 CTTAACCTAACAATTAAAACAACCCTTCATTAT
1 CTTAACCTAACAATTAAAACAACCCTTCATTAT
40565979 CTTAACCTAACAATTAAAACAACCCTTCATTAT
1 CTTAACCTAACAATTAAAACAACCCTTCATTAT
40566012 AAACTTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.42, C:0.27, G:0.00, T:0.30
Consensus pattern (33 bp):
CTTAACCTAACAATTAAAACAACCCTTCATTAT
Found at i:40570316 original size:23 final size:23
Alignment explanation
Indices: 40570293--40570338 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40570283 TTTTTCTATT
*
40570293 ATAAAAATATAATTTATTTAATTA
1 ATAAAAATA-AATTTAGTTAATTA
*
40570317 ATTAAAATAAATTTAGTTAATT
1 ATAAAAATAAATTTAGTTAATT
40570339 TACTCAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (23 bp):
ATAAAAATAAATTTAGTTAATTA
Found at i:40578703 original size:31 final size:31
Alignment explanation
Indices: 40578665--40578743 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
40578655 TTTAATGGTT
*
40578665 ACTGGGCCGAAGCTTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
40578696 ACTGGGCCAAAGCCTTTTCATAAATCATTTC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
40578727 ACTGGGCTGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
40578744 ACTGTAAATG
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.32
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:40578814 original size:42 final size:42
Alignment explanation
Indices: 40578767--40578858 Score: 148
Period size: 42 Copynumber: 2.2 Consensus size: 42
40578757 TGGCCTATAG
* ** *
40578767 GCCCATTTCAATATCACATGTAATGTCAATGGATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
40578809 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
1 GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
40578851 GCCCATTT
1 GCCCATTT
40578859 GGGGAGACTA
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.14, T:0.29
Consensus pattern (42 bp):
GCCCATTTCAATATCACATGAAATACCAATGAATGTATGCAA
Found at i:40579048 original size:26 final size:26
Alignment explanation
Indices: 40579003--40579100 Score: 146
Period size: 26 Copynumber: 3.8 Consensus size: 26
40578993 CCTATTTAAT
40579003 AACTGGGGCA-AAGCCCTTTTCGATA
1 AACTGGGGCATAAGCCCTTTTCGATA
*
40579028 AACTGGGGCATAAGCCCTTTTCAATA
1 AACTGGGGCATAAGCCCTTTTCGATA
*
40579054 AACTAGGGCATAAGCCCTTTTCTG-TA
1 AACTGGGGCATAAGCCCTTTTC-GATA
*
40579080 AACTGGGGTATAAGCCCTTTT
1 AACTGGGGCATAAGCCCTTTT
40579101 GCACTTCCTC
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
25 10 0.15
26 56 0.85
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (26 bp):
AACTGGGGCATAAGCCCTTTTCGATA
Found at i:40579945 original size:27 final size:27
Alignment explanation
Indices: 40579908--40579986 Score: 124
Period size: 27 Copynumber: 2.9 Consensus size: 27
40579898 TATTCATCAT
*
40579908 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGGTCAC
40579935 TTTACCCTACAGGGGCTTTACGGTCAC
1 TTTACCCTACAGGGGCTTTACGGTCAC
*
40579962 TTTATCCTACAGGGGCTTTACGGTC
1 TTTACCCTACAGGGGCTTTACGGTC
40579987 TTTTTACCTA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 48 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.25, G:0.23, T:0.32
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGGTCAC
Found at i:40579992 original size:27 final size:26
Alignment explanation
Indices: 40579908--40579996 Score: 117
Period size: 27 Copynumber: 3.3 Consensus size: 26
40579898 TATTCATCAT
40579908 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACC-TACAGGGGCT-TTACGGTCAC
40579935 TTTACCCTACAGGGGCTTTACGGTCAC
1 TTTA-CCTACAGGGGCTTTACGGTCAC
**
40579962 TTTATCCTACAGGGGCTTTACGGTCTT
1 TTTA-CCTACAGGGGCTTTACGGTCAC
40579989 TTTACCTA
1 TTTACCTA
40579997 ATAGGGGTAT
Statistics
Matches: 57, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
26 4 0.07
27 50 0.88
28 3 0.05
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.35
Consensus pattern (26 bp):
TTTACCTACAGGGGCTTTACGGTCAC
Found at i:40580078 original size:27 final size:27
Alignment explanation
Indices: 40580047--40580303 Score: 133
Period size: 27 Copynumber: 9.5 Consensus size: 27
40580037 GGTAAATCTA
40580047 CAAACCAAGGGTATTTCAGTAATTTTG
1 CAAACCAAGGGTATTTCAGTAATTTTG
* * *
40580074 TAAACTAATGGTATTTCTA-TAATTTTAG
1 CAAACCAAGGGTATTTC-AGTAATTTT-G
* ** *
40580102 -AAAGTCAAGGGTATTTTTGTAACTTTG
1 CAAA-CCAAGGGTATTTCAGTAATTTTG
* * * ** *
40580129 TAAATCAGGGGTATTTTGGTAATTTTA
1 CAAACCAAGGGTATTTCAGTAATTTTG
** * **
40580156 CAAATTAAGGGTATTTCGGTAATTTCA
1 CAAACCAAGGGTATTTCAGTAATTTTG
** *
40580183 CAAACCAAGGGTATTTTGGTAATTTTA
1 CAAACCAAGGGTATTTCAGTAATTTTG
* * * ** *
40580210 CAAACTAGGGGTGTTTTGGTAATTTTA
1 CAAACCAAGGGTATTTCAGTAATTTTG
*
40580237 CAAACCAAGGGTATCTT-AATAATTTTG
1 CAAACCAAGGGTAT-TTCAGTAATTTTG
* * * ***
40580264 TAAATCGAGGGTAAAACAGTAATTTTG
1 CAAACCAAGGGTATTTCAGTAATTTTG
* *
40580291 TAAATCAAGGGTA
1 CAAACCAAGGGTA
40580304 AAACAGTAAT
Statistics
Matches: 184, Mismatches: 39, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
27 162 0.88
28 22 0.12
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.37
Consensus pattern (27 bp):
CAAACCAAGGGTATTTCAGTAATTTTG
Found at i:40580115 original size:55 final size:54
Alignment explanation
Indices: 40580025--40580303 Score: 195
Period size: 54 Copynumber: 5.1 Consensus size: 54
40580015 TTTCATCCTA
* * * * *
40580025 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAA-
1 CAAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTCAGTAATTTTGTAAAT
* * ** *
40580078 CTAATGGTATTTCT-ATAATTTTAGAAAGTCAAGGGTATTTTTGTAACTTTGTAAAT
1 C-AAGGGTATTT-TGATAATTTTACAAA-TCAAGGGTATTTCAGTAATTTTGTAAAT
* * * * *** *
40580134 CAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTCAGTAATTTTGTAAAT
* * * ** ** *
40580188 CAAGGGTATTTTGGTAATTTTACAAA-CTAGGGGTGTTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGATAATTTTACAAATC-AAGGGTATTTCAGTAATTTTGTAAAT
* * ** * ***
40580242 CAAGGGTATCTTAATAATTTTGTAAATCGAGGGTAAAACAGTAATTTTGTAAAT
1 CAAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTCAGTAATTTTGTAAAT
40580296 CAAGGGTA
1 CAAGGGTA
40580304 AAACAGTAAT
Statistics
Matches: 175, Mismatches: 44, Indels: 13
0.75 0.19 0.06
Matches are distributed among these distances:
53 1 0.01
54 129 0.74
55 44 0.25
56 1 0.01
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.37
Consensus pattern (54 bp):
CAAGGGTATTTTGATAATTTTACAAATCAAGGGTATTTCAGTAATTTTGTAAAT
Found at i:40580195 original size:54 final size:54
Alignment explanation
Indices: 40580025--40580250 Score: 202
Period size: 54 Copynumber: 4.2 Consensus size: 54
40580015 TTTCATCCTA
* * * * **
40580025 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAATTTTACAAAC
* * * * * ** * ** *
40580079 TAATGGTATTTCT-ATAATTTTAGAAAGTCAAGGGTATTTTTGTAACTTTGTAAAT
1 CAAGGGTATTT-TGGTAATTTTACAAA-CCAAGGGTATTTCGGTAATTTTACAAAC
* ** *
40580134 CAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAATTTTACAAAC
* * * *
40580188 CAAGGGTATTTTGGTAATTTTACAAACTAGGGGTGTTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAATTTTACAAAC
40580242 CAAGGGTAT
1 CAAGGGTAT
40580251 CTTAATAATT
Statistics
Matches: 138, Mismatches: 31, Indels: 6
0.79 0.18 0.03
Matches are distributed among these distances:
54 95 0.69
55 43 0.31
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCGGTAATTTTACAAAC
Found at i:40580227 original size:81 final size:81
Alignment explanation
Indices: 40580025--40580250 Score: 231
Period size: 82 Copynumber: 2.8 Consensus size: 81
40580015 TTTCATCCTA
* * * * ** ** *
40580025 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACTAATGGTATTT
1 CAAGGGTATTTTGGTAATTTTACAAA-CAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTT
* * * *
40580090 CTATAATTTTAGAAAGT
65 CGATAATTTCACAAAGC
* * *
40580107 CAAGGGTATTTTTGTAACTTTGTA-AATCAGGGGTATTTTGGTAATTTTACAAATTAAGGGTATT
1 CAAGGGTATTTTGGTAA-TTT-TACAAACAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATT
*
40580171 TCGGTAATTTCACAAA-C
64 TCGATAATTTCACAAAGC
* *
40580188 CAAGGGTATTTTGGTAATTTTACAAACTAGGGGTGTTTTGGTAATTTTACAAACCAAGGGTAT
1 CAAGGGTATTTTGGTAATTTTACAAAC-AGGGGTATTTTGGTAATTTTACAAACTAAGGGTAT
40580251 CTTAATAATT
Statistics
Matches: 118, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
79 2 0.02
80 6 0.05
81 48 0.41
82 57 0.48
83 3 0.03
84 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (81 bp):
CAAGGGTATTTTGGTAATTTTACAAACAGGGGTATTTTGGTAATTTTACAAACTAAGGGTATTTC
GATAATTTCACAAAGC
Found at i:40580260 original size:81 final size:81
Alignment explanation
Indices: 40580055--40580261 Score: 204
Period size: 81 Copynumber: 2.5 Consensus size: 81
40580045 TACAAACCAA
** ** * * * * * * *
40580055 GGGTATTTCAGTAATTTTGTAAACTAATGGTATTTCTATAATTTTAGAAAGTCAAGGGTATTTTT
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAATAATTTCACAAA-CCAAGGGTATTTTG
*
40580120 GTAACTTTGTAAATCAG
65 GTAACTTTGTAAAACAG
** **
40580137 GGGTATTTTGGTAATTTTACAAATTAAGGGTATTTCGGTAATTTCACAAACCAAGGGTATTTTGG
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAATAATTTCACAAACCAAGGGTATTTTGG
40580202 TAA-TTT-TACAAACTAG
66 TAACTTTGTA-AAAC-AG
*
40580218 GGGTGTTTTGGTAATTTTACAAACCAAGGGTATCTT-AATAATTT
1 GGGTATTTTGGTAATTTTACAAACCAAGGGTAT-TTCAATAATTT
40580262 TGTAAATCGA
Statistics
Matches: 104, Mismatches: 18, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 2 0.02
80 6 0.06
81 54 0.52
82 42 0.40
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (81 bp):
GGGTATTTTGGTAATTTTACAAACCAAGGGTATTTCAATAATTTCACAAACCAAGGGTATTTTGG
TAACTTTGTAAAACAG
Found at i:40580304 original size:27 final size:27
Alignment explanation
Indices: 40580256--40580519 Score: 273
Period size: 27 Copynumber: 9.8 Consensus size: 27
40580246 GGTATCTTAA
*
40580256 TAATTTTGTAAATCGAGGGTAAAACAG
1 TAATTATGTAAATCGAGGGTAAAACAG
* *
40580283 TAATTTTGTAAATCAAGGGTAAAACAG
1 TAATTATGTAAATCGAGGGTAAAACAG
* *
40580310 TAATTCTATAAATCGAGGGTAAAACAG
1 TAATTATGTAAATCGAGGGTAAAACAG
* * **
40580337 TAATTCTATAAATCGAGGGT-AAAGTG
1 TAATTATGTAAATCGAGGGTAAAACAG
* **
40580363 ATAATTCTGTAAATCGAGGGTAAAATGG
1 -TAATTATGTAAATCGAGGGTAAAACAG
* * * **
40580391 TAATTACGTAAATTGGGGGTAAAATGG
1 TAATTATGTAAATCGAGGGTAAAACAG
40580418 TAATTATGTAAATC-AGAGGTAAAACAG
1 TAATTATGTAAATCGAG-GGTAAAACAG
*
40580445 TAATTATGTAAATC-AGGGGTAAAACGG
1 TAATTATGTAAATCGA-GGGTAAAACAG
* * **
40580472 TAATTATGTAAATCGAAGGTAGAATGG
1 TAATTATGTAAATCGAGGGTAAAACAG
*
40580499 TAATTTTGTAAATCGAGGGTA
1 TAATTATGTAAATCGAGGGTA
40580520 CTTTTGTAAT
Statistics
Matches: 208, Mismatches: 24, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
26 5 0.02
27 197 0.95
28 6 0.03
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (27 bp):
TAATTATGTAAATCGAGGGTAAAACAG
Found at i:40580528 original size:27 final size:26
Alignment explanation
Indices: 40580498--40580614 Score: 101
Period size: 27 Copynumber: 4.3 Consensus size: 26
40580488 AGGTAGAATG
** * *
40580498 GTAATTTTGTAAATCGAGGGTACTTTT
1 GTAATTTTACAAATCGAAGGTA-TTTA
*
40580525 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTT-A
*
40580552 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTT-A
* * *
40580579 GTATTTTTACAAA-CCAAGGGTATTTC
1 GTAATTTTACAAATCGAA-GGTATTTA
40580605 GATAATTTTA
1 G-TAATTTTA
40580615 GTAAACTAAA
Statistics
Matches: 75, Mismatches: 12, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
26 6 0.08
27 69 0.92
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (26 bp):
GTAATTTTACAAATCGAAGGTATTTA
Found at i:40580530 original size:81 final size:81
Alignment explanation
Indices: 40580256--40580519 Score: 309
Period size: 81 Copynumber: 3.3 Consensus size: 81
40580246 GGTATCTTAA
* * * * *
40580256 TAATTTTGTAAATCGAGGGTAAAACAGTAATTTTGTAAATCAAGGGTAAAACAGTAATTCTATAA
1 TAATTTTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAA
**
40580321 ATCGAGGGTAAAACAG
66 ATCGAGGGTAAAATGG
* * ** * * *
40580337 TAATTCTATAAATCGAGGGT-AAAGTGATAATTCTGTAAATC-GAGGGTAAAATGGTAATTACGT
1 TAATTTTGTAAATCGAGGGTAAAACAG-TAATTATGTAAATCAG-GGGTAAAACGGTAATTATGT
* *
40580400 AAATTGGGGGTAAAATGG
64 AAATCGAGGGTAAAATGG
*
40580418 TAATTATGTAAATC-AGAGGTAAAACAGTAATTATGTAAATCAGGGGTAAAACGGTAATTATGTA
1 TAATTTTGTAAATCGAG-GGTAAAACAGTAATTATGTAAATCAGGGGTAAAACGGTAATTATGTA
* *
40580482 AATCGAAGGTAGAATGG
65 AATCGAGGGTAAAATGG
40580499 TAATTTTGTAAATCGAGGGTA
1 TAATTTTGTAAATCGAGGGTA
40580520 CTTTTGTAAT
Statistics
Matches: 150, Mismatches: 27, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
80 6 0.04
81 137 0.91
82 7 0.05
ACGTcount: A:0.41, C:0.07, G:0.23, T:0.29
Consensus pattern (81 bp):
TAATTTTGTAAATCGAGGGTAAAACAGTAATTATGTAAATCAGGGGTAAAACGGTAATTATGTAA
ATCGAGGGTAAAATGG
Found at i:40580601 original size:54 final size:53
Alignment explanation
Indices: 40580498--40580614 Score: 130
Period size: 54 Copynumber: 2.2 Consensus size: 53
40580488 AGGTAGAATG
** * * *
40580498 GTAATTTTGTAAATCGAGGGTACTTTTGTAATTTTACAAGTCGAAGGTATTTC
1 GTAATTTTACAAATCGAGGGTACTTTAGTAATTTTACAAGACCAAGGTATTTC
*
40580551 AGTAATTTTACAAATCGAGGGTA-TTTCAGTATTTTTACAA-ACCAAGGGTATTTC
1 -GTAATTTTACAAATCGAGGGTACTTT-AGTAATTTTACAAGACCAA-GGTATTTC
40580605 GATAATTTTA
1 G-TAATTTTA
40580615 GTAAACTAAA
Statistics
Matches: 54, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
53 7 0.13
54 47 0.87
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (53 bp):
GTAATTTTACAAATCGAGGGTACTTTAGTAATTTTACAAGACCAAGGTATTTC
Found at i:40583970 original size:42 final size:42
Alignment explanation
Indices: 40583858--40583989 Score: 133
Period size: 44 Copynumber: 3.0 Consensus size: 42
40583848 CCGATATGTG
*
40583858 TTTTCGTGTAAGACCATG-TCTGGGACGTTGGCATCG-ACTTATGA
1 TTTT-GTGTAAGACCATGTTC-GGGACATTGGCATCGTA-TT-TGA
* * * *
40583902 TTTACGTGTACGACCATGTTTGGGACATTGGCATTGTATTTGA
1 TTT-TGTGTAAGACCATGTTCGGGACATTGGCATCGTATTTGA
* *
40583945 TTTTGTGTAAGACCCTGTTCGGGACAGTGGCATCGATATTTGA
1 TTTTGTGTAAGACCATGTTCGGGACATTGGCATCG-TATTTGA
40583988 TT
1 TT
40583990 ACATGTCAGA
Statistics
Matches: 73, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
42 26 0.36
43 15 0.21
44 30 0.41
45 2 0.03
ACGTcount: A:0.20, C:0.16, G:0.27, T:0.37
Consensus pattern (42 bp):
TTTTGTGTAAGACCATGTTCGGGACATTGGCATCGTATTTGA
Found at i:40591599 original size:27 final size:27
Alignment explanation
Indices: 40591490--40591601 Score: 145
Period size: 27 Copynumber: 4.1 Consensus size: 27
40591480 CACACGGGCT
*
40591490 TGTGGTAAAATGACTATTTTGCCCCTAA
1 TGTGGTAAAATGACTGTTTTGCCCCT-A
* * * *
40591518 T-TGATAAAATGATTGTTTTGCCCTTG
1 TGTGGTAAAATGACTGTTTTGCCCCTA
* *
40591544 TGTGGTAAAATGATTGTTTTGCCCTTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
40591571 TGTGGTAAAATGACTGTTTTGCCCCTA
1 TGTGGTAAAATGACTGTTTTGCCCCTA
40591598 TGTG
1 TGTG
40591602 ATATATGGTT
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
26 1 0.01
27 72 0.97
28 1 0.01
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.41
Consensus pattern (27 bp):
TGTGGTAAAATGACTGTTTTGCCCCTA
Found at i:40595127 original size:27 final size:27
Alignment explanation
Indices: 40595088--40595406 Score: 301
Period size: 27 Copynumber: 11.9 Consensus size: 27
40595078 CCAAATTAAT
* *
40595088 AAATGACTATTTTTCCCTTATGTGGTA
1 AAATGACTGTTTTGCCCTTATGTGGTA
40595115 AAATGACTGTTTTGCCCTTATGTGGTA
1 AAATGACTGTTTTGCCCTTATGTGGTA
* * *
40595142 AAATGATTGTTTTGACCCTAAT-TGATAA
1 AAATGACTGTTTTG-CCCTTATGTGGT-A
* *
40595170 AAATGAC---TTTGCCCCTA-GTTGATA
1 AAATGACTGTTTTGCCCTTATG-TGGTA
* * *
40595194 AAATAACTGTTTTGCCATTATGTGGTC
1 AAATGACTGTTTTGCCCTTATGTGGTA
* *
40595221 AAATGACTGTTTTGCCCCTA-GTTGATA
1 AAATGACTGTTTTGCCCTTATG-TGGTA
* * * *
40595248 TAATAACTGTTTTGCTCTTATATGGTA
1 AAATGACTGTTTTGCCCTTATGTGGTA
* *
40595275 AAATGTCTGTTTTGCCCTTATGTGATA
1 AAATGACTGTTTTGCCCTTATGTGGTA
* * * *
40595302 AAATGATTATTTTGCCCCTAAT-TGATA
1 AAATGACTGTTTTG-CCCTTATGTGGTA
* *
40595329 AAATAACTATTTTGCCCTTATGTGGTA
1 AAATGACTGTTTTGCCCTTATGTGGTA
40595356 AAATGACTGTTTTGCCCTTATGTGGTA
1 AAATGACTGTTTTGCCCTTATGTGGTA
* * *
40595383 AAATGATTATTTTGCCCCTATGTG
1 AAATGACTGTTTTGCCCTTATGTG
40595407 ATATATGGTT
Statistics
Matches: 237, Mismatches: 43, Indels: 24
0.78 0.14 0.08
Matches are distributed among these distances:
24 11 0.05
25 8 0.03
26 7 0.03
27 191 0.81
28 20 0.08
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (27 bp):
AAATGACTGTTTTGCCCTTATGTGGTA
Found at i:40595298 original size:81 final size:81
Alignment explanation
Indices: 40595097--40595411 Score: 406
Period size: 81 Copynumber: 3.9 Consensus size: 81
40595087 TAAATGACTA
* * *
40595097 TTTTTCCCTTATGTGGTAAAATGACTGTTTTGCCCTTATGTGGTAAAATGATTGTTTTGACCCTA
1 TTTTGCCCTTATGTGGTAAAATGACTGTTTTGCCCTTATGTGGTAAAATGATTATTTTGCCCCTA
40595162 ATTGATA-AA-AA-TG
66 ATTGATATAATAACTG
* * * * * * * *
40595175 ACTTTGCCCCTA-GTTGATAAAATAACTGTTTTGCCATTATGTGGTCAAATGACTGTTTTGCCCC
1 -TTTTGCCCTTATG-TGGTAAAATGACTGTTTTGCCCTTATGTGGTAAAATGATTATTTTGCCCC
*
40595239 TAGTTGATATAATAACTG
64 TAATTGATATAATAACTG
* * * *
40595257 TTTTGCTCTTATATGGTAAAATGTCTGTTTTGCCCTTATGTGATAAAATGATTATTTTGCCCCTA
1 TTTTGCCCTTATGTGGTAAAATGACTGTTTTGCCCTTATGTGGTAAAATGATTATTTTGCCCCTA
* *
40595322 ATTGATAAAATAACTA
66 ATTGATATAATAACTG
40595338 TTTTGCCCTTATGTGGTAAAATGACTGTTTTGCCCTTATGTGGTAAAATGATTATTTTGCCCCT-
1 TTTTGCCCTTATGTGGTAAAATGACTGTTTTGCCCTTATGTGGTAAAATGATTATTTTGCCCCTA
40595402 ATGTGATATA
66 AT-TGATATA
40595412 TGGTTATATT
Statistics
Matches: 200, Mismatches: 30, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
78 1 0.00
79 60 0.30
80 4 0.02
81 133 0.67
82 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.42
Consensus pattern (81 bp):
TTTTGCCCTTATGTGGTAAAATGACTGTTTTGCCCTTATGTGGTAAAATGATTATTTTGCCCCTA
ATTGATATAATAACTG
Found at i:40597906 original size:29 final size:27
Alignment explanation
Indices: 40597806--40597895 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
40597796 AGGAAGCATC
40597806 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
40597834 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
40597861 CTGGTGGCACTGCCACAGAATATCTGTAT
1 CTGGTGGCACTGCCACA-AATATCTGT-T
40597890 CTGGTG
1 CTGGTG
40597896 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:40597914 original size:55 final size:56
Alignment explanation
Indices: 40597806--40597920 Score: 139
Period size: 55 Copynumber: 2.1 Consensus size: 56
40597796 AGGAAGCATC
*
40597806 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACATATATCTGT-T
1 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
40597861 CTGGTGGC-ACTGCCACAGAA-TATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACA-AATTATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
40597917 CTGG
1 CTGG
40597921 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
54 1 0.02
55 28 0.54
56 23 0.44
ACGTcount: A:0.18, C:0.24, G:0.23, T:0.35
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:40598382 original size:19 final size:19
Alignment explanation
Indices: 40598358--40598396 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
40598348 TTTTAATTAT
* *
40598358 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
40598377 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
40598396 T
1 T
40598397 ATGATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:40604368 original size:12 final size:13
Alignment explanation
Indices: 40604340--40604372 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
40604330 TTATTTCTTT
40604340 TTCTCCATCTACC
1 TTCTCCATCTACC
*
40604353 TTCTCC-TCTTCC
1 TTCTCCATCTACC
40604365 TTCTCCAT
1 TTCTCCAT
40604373 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:40605525 original size:27 final size:27
Alignment explanation
Indices: 40605467--40605556 Score: 119
Period size: 28 Copynumber: 3.2 Consensus size: 27
40605457 AGGAAGCGTC
40605467 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAA-TATCTGTT
* *
40605495 CTGGTGGCCCTGCCACATATATCTGTT
1 CTGGTGGCACTGCCACAAATATCTGTT
40605522 CTGGTGGCACTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCAC-AAATATCTGT-T
40605551 CTGGTG
1 CTGGTG
40605557 ACTCTGTCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (27 bp):
CTGGTGGCACTGCCACAAATATCTGTT
Found at i:40606043 original size:19 final size:19
Alignment explanation
Indices: 40606019--40606057 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
40606009 TTTTAATTAT
* *
40606019 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
40606038 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
40606057 T
1 T
40606058 ATGATAAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:40608501 original size:42 final size:43
Alignment explanation
Indices: 40608454--40608536 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
40608444 CGTACAACCA
* *
40608454 TGTTTGGGACA-TCGGCATCG-TATTTGATTTCTTGTAAGACAC
1 TGTTTGGGACAGT-GGCATCGATATTTGATTACATGTAAGACAC
40608496 TGTTTGGGACAGTGGCATCGATATTTGATTACATGTAAGAC
1 TGTTTGGGACAGTGGCATCGATATTTGATTACATGTAAGAC
40608537 TACGACTGGG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
42 18 0.49
43 19 0.51
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.36
Consensus pattern (43 bp):
TGTTTGGGACAGTGGCATCGATATTTGATTACATGTAAGACAC
Found at i:40608547 original size:43 final size:42
Alignment explanation
Indices: 40608458--40608547 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 42
40608448 CAACCATGTT
* * **
40608458 TGGGACATCGGCATCGTATTTGATTTCTTGTAAGACACTGTT
1 TGGGACATCGGCATCGTATTTGATTACATGTAAGACACTGAC
40608500 TGGGACAGT-GGCATCGATATTTGATTACATGTAAGACTAC-GAC
1 TGGGACA-TCGGCATCG-TATTTGATTACATGTAAGAC-ACTGAC
40608543 TGGGA
1 TGGGA
40608548 TGTTGGCATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
42 14 0.34
43 25 0.61
44 2 0.05
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.32
Consensus pattern (42 bp):
TGGGACATCGGCATCGTATTTGATTACATGTAAGACACTGAC
Found at i:40611463 original size:12 final size:12
Alignment explanation
Indices: 40611446--40611470 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40611436 TTTTGGATGA
40611446 ATTTGATTGAAT
1 ATTTGATTGAAT
40611458 ATTTGATTGAAT
1 ATTTGATTGAAT
40611470 A
1 A
40611471 ATTTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (12 bp):
ATTTGATTGAAT
Found at i:40616205 original size:40 final size:40
Alignment explanation
Indices: 40615993--40616198 Score: 326
Period size: 40 Copynumber: 5.2 Consensus size: 40
40615983 AACCCAAGTA
* * * *
40615993 CCTTCGGAATTTAG-CCGGATATAG-CAACTCGCACGAATG
1 CCTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATG
* *
40616032 CCTTCAGGACTTAGCCCGGACATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40616072 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40616112 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
*
40616152 CCTTCGGGACTTAGCCCGGATATAATCACTAGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
40616192 CCTTCGG
1 CCTTCGG
40616199 ATCTTAGTCC
Statistics
Matches: 156, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 11 0.07
40 144 0.92
41 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATG
Found at i:40618069 original size:22 final size:23
Alignment explanation
Indices: 40618024--40618069 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
40618014 GACCTCGGAG
* * *
40618024 GGATTTATTACGTGCGAAGGATC
1 GGATCTATAACGTGCGAAGCATC
40618047 GGATCTATAACGT-CGAAGCATC
1 GGATCTATAACGTGCGAAGCATC
40618069 G
1 G
40618070 AAACATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.28, C:0.17, G:0.28, T:0.26
Consensus pattern (23 bp):
GGATCTATAACGTGCGAAGCATC
Found at i:40620530 original size:40 final size:40
Alignment explanation
Indices: 40620486--40620630 Score: 272
Period size: 40 Copynumber: 3.6 Consensus size: 40
40620476 GCTACTAGCT
40620486 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
40620526 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
* *
40620566 CAAATGCCTTCGGGACTTAGCCCGGTTGTAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
40620606 CAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG
40620631 GTATCAATCC
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 103 1.00
ACGTcount: A:0.23, C:0.28, G:0.24, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:40624511 original size:40 final size:40
Alignment explanation
Indices: 40624467--40624678 Score: 300
Period size: 40 Copynumber: 5.3 Consensus size: 40
40624457 GCTCCTCGTT
* ** *
40624467 CAAATGCCTTCGGGACATGGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAAT-TAGTAACTCGCA
*
40624507 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
* *
40624547 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCACA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
*
40624587 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
** *
40624627 CAAATGCCTTCGGGACTTAACTTGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
*
40624667 CAAAGGCCTTCG
1 CAAATGCCTTCG
40624679 AATCTTAGTC
Statistics
Matches: 161, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 159 0.99
41 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGAATTAGTAACTCGCA
Found at i:40624571 original size:80 final size:80
Alignment explanation
Indices: 40624467--40624732 Score: 313
Period size: 80 Copynumber: 3.3 Consensus size: 80
40624457 GCTCCTCGTT
* ** * *
40624467 CAAATGCCTTCGGGACATGGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAACCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGGACTTAACCCG
40624531 GATTTAGTAACTCGCA
65 GATTTAGTAACTCGCA
*
40624547 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCACACAAATGCCTTCGGGACTTAACCCGG
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGG
* *
40624612 AATTAGTATCTCGCA
66 ATTTAGTAACTCGCA
** * * **
40624627 CAAATGCCTTCGGGACTTAACTTGGAATTAGTATCTCGCACAAAGGCCTTC-GAATCTTAGTCCG
1 CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAATGCCTTCGGGA-CTTAACCCG
* * * *
40624691 GATATGGTCACTTAGCA
65 GATTTAGTAAC-TCGCA
*
40624708 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
40624733 CATCATTCAA
Statistics
Matches: 159, Mismatches: 24, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
79 2 0.01
80 148 0.93
81 9 0.06
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.25
Consensus pattern (80 bp):
CAAATGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAATGCCTTCGGGACTTAACCCGG
ATTTAGTAACTCGCA
Done.